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Jiang L, Zhang G, Wang P, Niu X, Liu Q, Zhang S, Gao W, Li Y. Simultaneous detection of bovine viral diarrhea virus (BVDV) and bovine herpesvirus 1 (BoHV-1) using recombinase polymerase amplification. Sci Rep 2024; 14:10169. [PMID: 38702375 PMCID: PMC11068760 DOI: 10.1038/s41598-024-56869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/12/2024] [Indexed: 05/06/2024] Open
Abstract
Bovine viral diarrhea virus (BVDV) is considered to be the most common agent of severe diarrhea in cattle worldwide, causing fever, diarrhea, ulcers, and abortion. Bovine herpesvirus 1 (BoHV-1) is also a major bovine respiratory disease agent that spreads worldwide and causes extensive damage to the livestock industry. Recombinase polymerase amplification (RPA) is a novel nucleic acid amplification method with the advantages of high efficiency, rapidity and sensitivity, which has been widely used in the diagnosis of infectious diseases. A dual RPA assay was developed for the simultaneous detection of BVDV and BoHV-1. The assay was completed at a constant temperature of 37 °C for 30 min. It was highly sensitive and had no cross-reactivity with other common bovine viruses. The detection rate of BVDV RPA in clinical samples (36.67%) was higher than that of PCR (33.33%), the detection rate of BoHV-1 RPA and PCR were equal. Therefore, the established dual RPA assay for BVDV and BoHV-1 could be a potential candidate for use as an immediate diagnostic.
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Affiliation(s)
- Lingling Jiang
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Gang Zhang
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Pu Wang
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Xiaoxia Niu
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Qiang Liu
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Sinong Zhang
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Weifeng Gao
- School of Life Sciences, Ningxia University, Yinchuan, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China
| | - Yong Li
- School of Life Sciences, Ningxia University, Yinchuan, China.
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan, China.
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Liu Y, Xiang J, Gao Y, Wang J, Liu L, Li R, Wang J. Rapid detection of Cryptosporidium spp. in diarrheic cattle feces by isothermal recombinase polymerase amplification assays. Heliyon 2023; 9:e20794. [PMID: 37860527 PMCID: PMC10582492 DOI: 10.1016/j.heliyon.2023.e20794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 09/10/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
As a zoonotic parasite, Cryptosporidium spp. could cause severe diarrhea mainly in calves and children globally. Monitoring and prevention of Cryptosporidium spp.'s prevalence is of great significance in both economy and public health aspects. In this study, specific primers and probes were designed within the conserved region of 18S rRNA gene for Cryptosporidium spp. and recombinase polymerase amplification assays based on the fluorescence monitoring (real-time RPA) as well as combined with a lateral flow strip (LFS RPA) were developed. Both of the two RPA assays allowed the exponential amplification of the target fragment within 20 min. After incubation on a metal bath at 42 °C, the LFS RPA results were displayed on the lateral flow strip within 5 min while real-time RPA allowed the real-time observation of the results in Genie III at 39 °C. The RPA assays showed high specificity for Cryptosporidium spp. without any cross-reaction with other tested pathogens causing diarrhea in cattle. With the recombinant plasmid DNA containing the 18S rRNA gene of Cryptosporidium spp. serving as a template, the limit of detection for real-time RPA and LFS RPA assays were 14.6 and 12.7 copies/reaction, respectively. Moreover, the RPA assays were validated by testing diarrheic cattle fecal samples and compared with a real-time PCR. The positive ratio of Cryptosporidium spp. was 24.04 % (44/183) and 26.23 % (48/183) in both RPA assays and real-time PCR assay, respectively, and the kappa coefficient value was 0.942. The diagnostic specificity and diagnostic sensitivity of both RPA assays were 100 % and 91.67 %, respectively. Forty-one of 48 positive samples were successfully sequenced and four Cryptosporidium species were detected, including C. parvum (n = 20), C. andersoni (n = 17), C. bovis (n = 3) and C. ryanae (n = 1). The developed RPA assays are easy to operate and faster to obtain the detection results, and they are suiting for the point-of-care detection and facilitating the prevention and control of Cryptosporidium spp. infections.
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Affiliation(s)
- Yuelin Liu
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jialin Xiang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Yaxin Gao
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jinfeng Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Libing Liu
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
| | - Ruiwen Li
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Jianchang Wang
- Food Microbiology and Animal Quarantine Laboratory, Technology Center of Shijiazhuang Customs District, Shijiazhuang, China
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Hifumi T, Tanaka T, Sato M, Akioka K, Fujimata C, Miyoshi N. Rapid detection of alveolar echinococcosis in hepatic nodules of horses by recombinase polymerase amplification assay. Vet Anim Sci 2023; 20:100291. [PMID: 36936549 PMCID: PMC10015249 DOI: 10.1016/j.vas.2023.100291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Alveolar echinococcosis in slaughtered horses remains a public health issue. This study aimed to develop a Recombinase polymerase amplification (RPA) assay targeting the mitochondrial NADH dehydrogenase subunit 5 (Nad5) gene of Echinococcus multilocularis for the rapid detection of equine alveolar echinococcosis. Thirty-six hepatic solid nodules obtained from each horse (n = 36) were evaluated based on histopathological examination and Nad5-targeted PCR and then submitted to the RPA assay. The results of the developed RPA assay were 94.4% consistent with those of Nad5 PCR and Cohen's kappa coefficient value was 0.89 statistically, indicating high agreement. In addition, the RPA assay using the plasmid samples was one hundredfold more sensitive than PCR testing. Consequently, these results suggest that the performance of the RPA assay developed in this study is equal to that of conventional PCR testing.
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Affiliation(s)
- Tatsuro Hifumi
- Laboratory of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Corresponding author.
| | - Miho Sato
- Laboratory of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kohei Akioka
- Kumamoto Prefectural Meat Inspection Center, 1314 Sosaki, Shichijo-machi, Kikuchi, Kumamoto 861-1344, Japan
| | - Chiaki Fujimata
- Kumamoto Prefectural Meat Inspection Center, 1314 Sosaki, Shichijo-machi, Kikuchi, Kumamoto 861-1344, Japan
| | - Noriaki Miyoshi
- Laboratory of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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Jena S, Gaur D, Dubey NC, Tripathi BP. Advances in paper based isothermal nucleic acid amplification tests for water-related infectious diseases. Int J Biol Macromol 2023:125089. [PMID: 37245760 DOI: 10.1016/j.ijbiomac.2023.125089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/14/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Water-associated or water-related infectious disease outbreaks are caused by pathogens such as bacteria, viruses, and protozoa, which can be transmitted through contaminated water sources, poor sanitation practices, or insect vectors. Low- and middle-income countries bear the major burden of these infections due to inadequate hygiene and subpar laboratory facilities, making it challenging to monitor and detect infections in a timely manner. However, even developed countries are not immune to these diseases, as inadequate wastewater management and contaminated drinking water supplies can also contribute to disease outbreaks. Nucleic acid amplification tests have proven to be effective for early disease intervention and surveillance of both new and existing diseases. In recent years, paper-based diagnostic devices have made significant progress and become an essential tool in detecting and managing water-associated diseases. In this review, we highlight the importance of paper and its variants as a diagnostic tool and discuss the properties, design modifications, and various paper-based device formats developed and used for detecting water-associated pathogens.
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Affiliation(s)
- Saikrushna Jena
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Divya Gaur
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Nidhi C Dubey
- Department of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Bijay P Tripathi
- Department of Materials Science & Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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Bhat AI, Aman R, Mahfouz M. Onsite detection of plant viruses using isothermal amplification assays. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1859-1873. [PMID: 35689490 PMCID: PMC9491455 DOI: 10.1111/pbi.13871] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/16/2022] [Accepted: 06/02/2022] [Indexed: 05/09/2023]
Abstract
Plant diseases caused by viruses limit crop production and quality, resulting in significant losses. However, options for managing viruses are limited; for example, as systemic obligate parasites, they cannot be killed by chemicals. Sensitive, robust, affordable diagnostic assays are needed to detect the presence of viruses in plant materials such as seeds, vegetative parts, insect vectors, or alternative hosts and then prevent or limit their introduction into the field by destroying infected plant materials or controlling insect hosts. Diagnostics based on biological and physical properties are not very sensitive and are time-consuming, but assays based on viral proteins and nucleic acids are more specific, sensitive, and rapid. However, most such assays require laboratories with sophisticated equipment and technical skills. By contrast, isothermal-based assays such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) are simple, easy to perform, reliable, specific, and rapid and do not require specialized equipment or skills. Isothermal amplification assays can be performed using lateral flow devices, making them suitable for onsite detection or testing in the field. To overcome non-specific amplification and cross-contamination issues, isothermal amplification assays can be coupled with CRISPR/Cas technology. Indeed, the collateral activity associated with some CRISPR/Cas systems has been successfully harnessed for visual detection of plant viruses. Here, we briefly describe traditional methods for detecting viruses and then examine the various isothermal assays that are being harnessed to detect viruses.
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Affiliation(s)
- Alangar I. Bhat
- ICAR‐Indian Institute of Spices ResearchKozhikodeKeralaIndia
| | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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Du J, Ma B, Li J, Wang Y, Dou T, Xu S, Zhang M. Rapid Detection and Differentiation of Legionella pneumophila and Non-Legionella pneumophila Species by Using Recombinase Polymerase Amplification Combined With EuNPs-Based Lateral Flow Immunochromatography. Front Chem 2022; 9:815189. [PMID: 35198541 PMCID: PMC8859533 DOI: 10.3389/fchem.2021.815189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
Legionella, a waterborne pathogen, is the main cause of Legionnaires’ disease. Therefore, timely and accurate detection and differentiation of Legionella pneumophila and non-Legionella pneumophila species is crucial. In this study, we develop an easy and rapid recombinase polymerase amplification assay combined with EuNPs-based lateral flow immunochromatography (EuNPs-LFIC-RPA) to specifically distinguish Legionella pneumophila and non-Legionella pneumophila. We designed primers based on the mip gene of Legionella pneumophila and the 5S rRNA gene of non-Legionella pneumophila. The recombinase polymerase amplification reaction could go to completion in 10 min at 37°C, and the amplification products could be detected within 5 min with EuNPs-LFIC strips. Using a florescent test strip reader, the quantitative results were achieved by reading the colored signal intensities on the strips. The sensitivity was 1.6 × 101 CFU/ml, and a linear standard linear curve plotted from the test strip reader had a correlation coefficient for the determination of Legionella pneumophila (R2 = 0.9516). Completed concordance for the presence or absence of Legionella pneumophila by EuNPs-LFIC-RPA and qPCR was 97.32% (κ = 0.79, 95% CI), according to an analysis of practical water samples (n = 112). In short, this work shows the feasibility of EuNPs-LFIC-RPA for efficient and rapid monitoring of Legionella pneumophila and non-Legionella pneumophila in water samples.
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Panpru P, Srisrattakarn A, Panthasri N, Tippayawat P, Chanawong A, Tavichakorntrakool R, Daduang J, Wonglakorn L, Lulitanond A. Rapid detection of Enterococcus and vancomycin resistance using recombinase polymerase amplification. PeerJ 2021; 9:e12561. [PMID: 34966584 PMCID: PMC8663621 DOI: 10.7717/peerj.12561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/07/2021] [Indexed: 01/14/2023] Open
Abstract
Vancomycin-resistant enterococci (VRE), especially Enterococcus faecium, have been a global concern, often causing serious healthcare-associated infections. We established a rapid approach for detecting E. faecium and vancomycin-resistance genes (vanA and vanB) in clinical samples using isothermal recombinase polymerase amplification (RPA) combined with a lateral-flow (LF) strip. Specific RPA primer sets and probes for ddl (to identify the presence of E. faecium) vanA and vanB genes were designed. The RPA reaction was performed under isothermal condition at 37 °C within 20 min and read using the LF strip within a further 5 min. A total of 141 positive blood-cultures and 136 stool/rectal swab samples were tested using RPA-LF method compared to the conventional PCR method. The RPA-LF method exhibited 100% sensitivity in both blood-culture (60 E. faecium; 35 vanA type and two vanB type) and stool/rectal-swab samples (63 E. faecium and 36 vanA type) without cross-reaction (100% specificity). The lower detection limit of the RPA-LF was approximately 10 times better than that of the conventional PCR method. The RPA-LF method is an alternative rapid method with excellent sensitivity and specificity for detecting E. faecium, vanA, and vanB, and it has the potential to be used as a point-of-care device for VRE therapy and prevention.
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Affiliation(s)
- Pimchanok Panpru
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Arpasiri Srisrattakarn
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | | | - Patcharaporn Tippayawat
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Aroonwadee Chanawong
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Ratree Tavichakorntrakool
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Jureerut Daduang
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Lumyai Wonglakorn
- Clinical Microbiology Unit, Srinagarind Hospital, Khon Kaen University, Khon Kaen, Thailand
| | - Aroonlug Lulitanond
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
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Chu H, Liu C, Liu J, Yang J, Li Y, Zhang X. Recent advances and challenges of biosensing in point-of-care molecular diagnosis. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 348:130708. [PMID: 34511726 PMCID: PMC8424413 DOI: 10.1016/j.snb.2021.130708] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/07/2023]
Abstract
Molecular diagnosis, which plays a major role in infectious disease screening with successful understanding of the human genome, has attracted more attention because of the outbreak of COVID-19 recently. Since point-of-care testing (POCT) can expand the application of molecular diagnosis with the benefit of rapid reply, low cost, and working in decentralized environments, many researchers and commercial institutions have dedicated tremendous effort and enthusiasm to POCT-based biosensing for molecular diagnosis. In this review, we firstly summarize the state-of-the-art techniques and the construction of biosensing systems for POC molecular diagnosis. Then, the application scenarios of POCT-based biosensing for molecular diagnosis were also reviewed. Finally, several challenges and perspectives of POC biosensing for molecular diagnosis are discussed. This review is expected to help researchers deepen comprehension and make progresses in POCT-based biosensing field for molecular diagnosis applications.
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Affiliation(s)
- Hongwei Chu
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Conghui Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Jinsen Liu
- Shenzhen ENCO Instrument Co., Ltd, Shenzhen 518000, China
| | - Jiao Yang
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Yingchun Li
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, School of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong 518055, China
| | - Xueji Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
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Cantera JL, White HN, Forrest MS, Stringer OW, Belizario VY, Storey HL, de Hostos EL, de los Santos T. Sensitive and semiquantitative detection of soil-transmitted helminth infection in stool using a recombinase polymerase amplification-based assay. PLoS Negl Trop Dis 2021; 15:e0009782. [PMID: 34516554 PMCID: PMC8459997 DOI: 10.1371/journal.pntd.0009782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 09/23/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Background Soil-transmitted helminths (STHs) are parasitic nematodes that inhabit the human intestine. They affect more than 1.5 billion people worldwide, causing physical and cognitive impairment in children. The global strategy to control STH infection includes periodic mass drug administration (MDA) based on the results of diagnostic testing among populations at risk, but the current microscopy method for detecting infection has diminished sensitivity as the intensity of infection decreases. Thus, improved diagnostic tools are needed to support decision-making for STH control programs. Methodology We developed a nucleic acid amplification test based on recombinase polymerase amplification (RPA) technology to detect STH in stool. We designed primers and probes for each of the four STH species, optimized the assay, and then verified its performance using clinical stool samples. Principal findings Each RPA assay was as sensitive as a real-time polymerase chain reaction (PCR) assay in detecting copies of cloned target DNA sequences. The RPA assay amplified the target in DNA extracted from human stool samples that were positive for STH based on the Kato-Katz method, with no cross-reactivity of the non-target genomic DNA. When tested with clinical stool samples from patients with infections of light, moderate, and heavy intensity, the RPA assays demonstrated performance comparable to that of real-time PCR, with better results than Kato-Katz. This new rapid, sensitive and field-deployable method for detecting STH infections can help STH control programs achieve their goals. Conclusions Semi-quantitation of target by RPA assay is possible and is comparable to real-time PCR. With proper instrumentation, RPA assays can provide robust, semi-quantification of STH DNA targets as an alternative field-deployable indicator to counts of helminth eggs for assessing infection intensity. More than 1.5 billion people are infected with parasitic intestinal worms called soil-transmitted helminths. Infection is transmitted by helminth eggs in human feces, which contaminate soil in areas with poor sanitation. Adverse health effects include physical and cognitive impairment in children. A key strategy to control infection is periodic mass drug administration for populations with a high prevalence of disease based on the results of diagnostic testing. The current microscopy method for detecting infection, however, has limited ability to detect disease as the intensity of infection decreases with repeated mass drug administration. To address limitations of current diagnostic methods, we developed a novel technique to diagnose infections, including those at very low levels of intensity, by detecting helminth DNA in stool samples. Our initial studies suggest that the new diagnostic technique reliably detects the presence of intestinal worms, even at low intensities of infection, and may be more useful than currently available diagnostic tools for guiding the use of periodic mass drug administration to eliminate disease in low-resource settings.
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Affiliation(s)
| | | | | | | | - Vicente Y. Belizario
- Department of Parasitology, College of Public Health, University of the Philippines, Ermita, Manila, Philippines
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Wu YD, Wang QQ, Wang M, Elsheikha HM, Yang X, Hu M, Zhu XQ, Xu MJ. Development of a Lateral Flow Strip-Based Recombinase Polymerase Amplification Assay for the Detection of Haemonchus contortus in Goat Feces. THE KOREAN JOURNAL OF PARASITOLOGY 2021; 59:167-171. [PMID: 33951773 PMCID: PMC8106983 DOI: 10.3347/kjp.2021.59.2.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 02/04/2021] [Indexed: 11/23/2022]
Abstract
Haemonchosis remains a significant problem in small ruminants. In this study, the assay of recombinase polymerase amplification (RPA) combined with the lateral flow strip (LFS-RPA) was established for the rapid detection of Haemonchus contortus in goat feces. The assay used primers and a probe targeting a specific sequence in the ITS-2 gene. We compared the performance of the LFS-RPA assay to a PCR assay. The LFS-RPA had a detection limit of 10 fg DNA, which was 10 times less compared to the lowest detection limit obtained by PCR. Out of 24 goat fecal samples, LFS-RPA assay detected H. contortus DNA with 95.8% sensitivity, compared to PCR, 79.1% sensitivity. LFS-RPA assay did not detect DNA from other related helminth species and demonstrated an adequate tolerance to inhibitors present in the goat feces. Taken together, our results suggest that LFS-RPA assay had a high diagnostic accuracy for the rapid detection of H. contortus and merits further evaluation.
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Affiliation(s)
- Yao-Dong Wu
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.,State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Qi-Qi Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Meng Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Xin Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, PR China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei Province 430070, PR China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China.,College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province 030801, PR China
| | - Min-Jun Xu
- Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
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Nie Z, Zhao Y, Shu X, Li D, Ao Y, Li M, Wang S, Cui J, An X, Zhan X, He L, Liu Q, Zhao J. Recombinase polymerase amplification with lateral flow strip for detecting Babesia microti infections. Parasitol Int 2021; 83:102351. [PMID: 33872796 DOI: 10.1016/j.parint.2021.102351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/03/2020] [Accepted: 04/13/2021] [Indexed: 11/17/2022]
Abstract
Babesia microti is one of the most important pathogens causing humans and rodents babesiosis-an emerging tick-borne disease that occurs worldwide. At present, the gold standard for the detection of Babesia is the microscopic examination of blood smears, but this diagnostic test has several limitations. The recombinase polymerase amplification with lateral flow (LF-RPA) assay targeting the mitochondrial cytochrome oxidase subunit I (cox I) gene of B. microti was developed in this study. The LF-RPA can be performed within 10-30 min, at a wide range of temperatures between 25 and 45 °C, which is much faster and easier to perform than conventional PCR. The results showed that the LF-RAP can detect 0.25 parasites/μl blood, which is 40 times more sensitive than the conventional PCR based on the V4 variable region of 18S rRNA. Specificity assay showed no cross-reactions with DNAs of related apicomplexan parasites and their host. The applicability of the LF-RPA method was further evaluated using two clinical human samples and six experimental mice samples, with seven samples were positively detected, while only three of them were defined as positive by conventional PCR. These results present the developed LF-RPA as a new simple, specific, sensitive, rapid and convenient method for diagnosing infection with B. microti. This novel assay was the potential to be used in field applications and large-scale sample screening.
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Affiliation(s)
- Zheng Nie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Yangnan Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Xiang Shu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Dongfang Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Yangsiqi Ao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Muxiao Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Sen Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Jie Cui
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Xiaomeng An
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Xueyan Zhan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China
| | - Lan He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China.
| | - Qin Liu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Center for Tropical Diseases, Shanghai, China.
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Animal Epidemical Disease and Infectious Zoonoses, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan, Hubei 430070, China.
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12
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On point identification of species origin of food animals by recombinase polymerase amplification-lateral flow (RPA-LF) assay targeting mitochondrial gene sequences. Journal of Food Science and Technology 2020; 58:1286-1294. [PMID: 33746256 DOI: 10.1007/s13197-020-04637-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/29/2019] [Accepted: 07/08/2020] [Indexed: 01/08/2023]
Abstract
The present study was aimed to develop and standardize Recombinase polymerase amplification-lateral flow (RPA-LF) assays for on point identification of species origin of food animals viz: cattle, buffalo and pig. Species specific RPA primers sets for cattle, buffalo and pig were designed by homology comparisons of the sequences of mitochondrial cytochrome b gene and d-loop region from common food species viz: cattle, buffalo, sheep, goat, pig and chicken. The RPA assays for designed primers sets were optimized using the reaction components from Twist Amp basic kit and instructions in its manual. Endpoint detection of species specific amplified RPA products were made by gel electrophoresis and designed species specific RPA-LFA strips. The developed assays were evaluated for their specificity, diagnostic sensitivity, and validated on coded samples and binary meat admixtures with relative percentage of 20, 10, 5 & 1% target species. The developed RPA assays resulted in amplification of DNA template exclusively of cattle, buffalo and pig origin to product sizes of 294, 405 and 283 bp respectively. The diagnostic sensitivities of developed assays were up to 10 pg of genomic DNA and highly correlated with species specific PCR assays taken as gold standard. Developed species specific RPA assays also identified the target species in coded samples and binary meat admixture up to 1%.
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13
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Zhang Y, Hu J, Li Q, Guo J, Zhang G. Detection of microorganisms using recombinase polymerase amplification with lateral flow dipsticks. METHODS IN MICROBIOLOGY 2020. [DOI: 10.1016/bs.mim.2019.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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14
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Zhao J, Xu W, Tu G, Zhou Y, Wu X. Sensitive and rapid detection of Ortleppascaris sinensis (Nematoda: Ascaridoidea) by loop-mediated isothermal amplification. PeerJ 2019; 7:e7607. [PMID: 31534850 PMCID: PMC6733237 DOI: 10.7717/peerj.7607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/05/2019] [Indexed: 11/20/2022] Open
Abstract
Ortleppascaris sinensis is the dominant nematode species infecting the gastrointestinal tract of the captive Chinese alligator, a critically endangered species. Gastrointestinal nematode infection may cause a loss of appetite, growth, a development disorder, and even mortality in alligators, especially young ones. This research first establishment a loop-mediated isothermal amplification (LAMP) assay in rapidly identifying O. sinensis, upon the basis of the complete internal transcribed spacers (ITS) gene. Eight sets of primers were designed for recognition of the unique conserved ITS gene sequences, and one set was selected to be the most suitable primer for rapid detection. The specific as well as the sensitive features of the most appropriate primer in LAMP reactions for O. sinensis, and feces specimens of Chinese alligators suffering from O. sinensis were determined. Turbidity monitoring and Te Visual Reagent methods were used for determining negative and positive consequences. According to this study, amplification and visualization of the target DNA could be realized through two detection approaches during 50 min at 65 °C isothermal temperature. The sensitivity of LAMP was a detecting limitation of 3.46 pg/µl DNA. No cross-reactions were found between O. sinensis and any other of the nine heterologous nematode parasites, which shows the outstanding specific features of the primers. The LAMP assay could also perform a detection of target DNA of O. sinensis in the feces samples of Chinese alligators. This LAMP assay is useful for directly detecting O. sinensis in the Chinese alligator breeding centers, particularly due to its rapidity, simplicity and low cost.
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Affiliation(s)
- Jinhong Zhao
- Department of Parasitology, Wannan Medical College, Wuhu, Anhui, China.,Provincial Laboratory of Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Wei Xu
- Department of Parasitology, Wannan Medical College, Wuhu, Anhui, China
| | - Genjun Tu
- The National Nature Reserve of Chinese Alligator in Anhui, Xuanzhou, Anhui, China
| | - Yongkang Zhou
- The National Nature Reserve of Chinese Alligator in Anhui, Xuanzhou, Anhui, China
| | - Xiaobing Wu
- Provincial Laboratory of Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
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15
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Zhao G, He H, Wang H. Use of a recombinase polymerase amplification commercial kit for rapid visual detection of Pasteurella multocida. BMC Vet Res 2019; 15:154. [PMID: 31101109 PMCID: PMC6525368 DOI: 10.1186/s12917-019-1889-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background Pasteurella multocida (P. multocida) is a bacterium that causes bovine respiratory disease (BRD) and haemorrhagic septicaemia (HS) in cattle, buffaloes and bison. Rapid point-of-care diagnosis or regular testing of Pasteurellosis, therefore, could contribute greatly to early detection, and screening infected animal is important. Up to now, there are no published reports on the use of recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD) for P. multocida detection. Results This study proposes a promising isothermal detection method for P. multocida with the potential to be developed as an on-site test for Pasteurellosis. The method includes an RPA combined with LFD. First, the analytical sensitivity and specificity of P. multocida RPA-LFD were tested. The RPA-LFD, performed at 39 °C, successfully detected P. multocida DNA in 30 min, with a detection limit of up to 120 copies per reaction. Then, the practicability of RPA-LFD was analysed using 62 nasal swabs and 33 fresh lungs samples from 17 different dairy farms. Compared to real-time quantitative PCR (qPCR), the RPA-LFD assay yielded a clinical specificity of 95.15%, positive predictive value (PPV) of 95.15% and 0.958 kappa coefficient. Compared with the culture method, it achieved 100% sensitivity, 67.20% specificity and a 0.572 kappa coefficient. Conclusions These results combined with the simple conditions required for the performance of the RPA-LFD assay, have demonstrated the effectiveness and practicability of the method for development into a regular on-site protocol for the diagnosis of Pasteurellosis.
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Affiliation(s)
- Guimin Zhao
- Ruminant Disease Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, No.88 Wenhua East Road, Lixia District, Jinan, 250014, Shandong Province, China
| | - Hongbin He
- Ruminant Disease Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, No.88 Wenhua East Road, Lixia District, Jinan, 250014, Shandong Province, China.
| | - Hongmei Wang
- Ruminant Disease Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, No.88 Wenhua East Road, Lixia District, Jinan, 250014, Shandong Province, China.
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16
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Nelson MM, Waldron CL, Bracht JR. Rapid molecular detection of macrolide resistance. BMC Infect Dis 2019; 19:144. [PMID: 30755177 PMCID: PMC6373131 DOI: 10.1186/s12879-019-3762-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/30/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Emerging antimicrobial resistance is a significant threat to human health. However, methods for rapidly diagnosing antimicrobial resistance generally require multi-day culture-based assays. Macrolide efflux gene A, mef(A), provides resistance against erythromycin and azithromycin and is known to be laterally transferred among a wide range of bacterial species. METHODS We use Recombinase Polymerase Assay (RPA) to detect the antimicrobial resistance gene mef(A) from raw lysates without nucleic acid purification. To validate these results we performed broth dilution assays to assess antimicrobial resistance to erythromycin and ampicillin (a negative control). RESULTS We validate the detection of mef(A) in raw lysates of Streptococcus pyogenes, S. pneumoniae, S. salivarius, and Enterococcus faecium bacterial lysates within 7-10 min of assay time. We show that detection of mef(A) accurately predicts real antimicrobial resistance assessed by traditional culture methods, and that the assay is robust to high levels of spiked-in non-specific nucleic acid contaminant. The assay was unaffected by single-nucleotide polymorphisms within divergent mef(A) gene sequences, strengthening its utility as a robust diagnostic tool. CONCLUSIONS This finding opens the door to implementation of rapid genomic diagnostics in a clinical setting, while providing researchers a rapid, cost-effective tool to track antibiotic resistance in both pathogens and commensal strains.
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Affiliation(s)
- Megan M. Nelson
- Department of Biology, American University, Washington, DC 20016 USA
| | | | - John R. Bracht
- Department of Biology, American University, Washington, DC 20016 USA
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17
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Khan A, Shams S, Khan S, Khan MI, Khan S, Ali A. Evaluation of prevalence and risk factors associated with Cryptosporidium infection in rural population of district Buner, Pakistan. PLoS One 2019; 14:e0209188. [PMID: 30601870 PMCID: PMC6314602 DOI: 10.1371/journal.pone.0209188] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/30/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cryptosporidium spp are important intestinal protozoan parasites that cause diarrhea in humans, domestic and wild animals. Its infection remains a main public health concern however, the epidemics in human being is still unclear, particularly in developing countries. There are several factors that may enhance the spreading of this parasite in human population especially in young children. METHODOLOGY A questionnaire was designed to obtain the demographic and clinical data from the participants. A total of 425 stool samples were collected from suspected children (aged 3-10 years) in different hospitals and villages. The initial screening was performed with modified Ziehl Neelsen (mZN) staining technique followed by polymerase chain reaction (PCR). Several potential risk factors were also assessed through the obtained information from suspected individuals. RESULTS Out of all 425 collected samples, 127 were observed positive by mZN with a prevalence of 29.88% (127/425). The 127 mZN positive samples together with 50 mZN negative samples were processed for molecular analysis through PCR assay. Among them, 71 out of 127 mZN positive samples and 4 out of 50 mZN negative samples were found positive by PCR. The molecular analysis showed that Cryptosporidium parvum was the main cause of infection in children. The results revealed that individuals exposed to diarrhea were more likely to be infected with Cryptosporidium infection while several environmental factors may also play a key role in spreading of this parasite. CONCLUSIONS/SIGNIFICANCE OF THE STUDY The current high prevalence of Cryptosporidium infection may be due to the lack of awareness and routine based testing in identification of this parasite in District Buner. Further studies are required to determine the importance of Cryptosporidium infection in this area as well as across the country and to find out the possible risk factors that may be associated with the occurrence of this protozoan. There is, however, an urgent need for laboratory-based observational studies to develop a more dynamic estimate of the cryptosporidial disease burden in the region.
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Affiliation(s)
- Asar Khan
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sumaira Shams
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Saima Khan
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Iftikhar Khan
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
- Centre for Biotechnology and Microbiology University of Swat, Swat, Pakistan
| | - Sardar Khan
- Department of Environmental Science, University of Peshawar, Peshawar, Pakistan
| | - Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
- * E-mail:
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18
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Li J, Macdonald J, von Stetten F. Review: a comprehensive summary of a decade development of the recombinase polymerase amplification. Analyst 2019; 144:31-67. [DOI: 10.1039/c8an01621f] [Citation(s) in RCA: 240] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RPA is a versatile complement or replacement of PCR, and now is stepping into practice.
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Affiliation(s)
- Jia Li
- Laboratory for MEMS Applications
- IMTEK – Department of Microsystems Engineering
- University of Freiburg
- 79110 Freiburg
- Germany
| | - Joanne Macdonald
- Inflammation and Healing Research Cluster
- Genecology Research Centre
- School of Science and Engineering
- University of the Sunshine Coast
- Australia
| | - Felix von Stetten
- Laboratory for MEMS Applications
- IMTEK – Department of Microsystems Engineering
- University of Freiburg
- 79110 Freiburg
- Germany
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19
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Choi JR, Hu J, Gong Y, Feng S, Wan Abas WAB, Pingguan-Murphy B, Xu F. An integrated lateral flow assay for effective DNA amplification and detection at the point of care. Analyst 2018; 141:2930-9. [PMID: 27010033 DOI: 10.1039/c5an02532j] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Lateral flow assays (LFAs) have been extensively explored in nucleic acid testing (NAT) for medical diagnostics, food safety analysis and environmental monitoring. However, the amount of target nucleic acid in a raw sample is usually too low to be directly detected by LFAs, necessitating the process of amplification. Even though cost-effective paper-based amplification techniques have been introduced, they have always been separately performed from LFAs, hence increasing the risk of reagent loss and cross-contaminations. To date, integrating paper-based nucleic acid amplification into colorimetric LFA in a simple, portable and cost-effective manner has not been introduced. Herein, we developed an integrated LFA with the aid of a specially designed handheld battery-powered system for effective amplification and detection of targets in resource-poor settings. Interestingly, using the integrated paper-based loop-mediated isothermal amplification (LAMP)-LFA, we successfully performed highly sensitive and specific target detection, achieving a detection limit of as low as 3 × 10(3) copies of target DNA, which is comparable to the conventional tube-based LAMP-LFA in an unintegrated format. The device may serve in conjunction with a simple paper-based sample preparation to create a fully integrated paper-based sample-to-answer diagnostic device for point-of-care testing (POCT) in the near future.
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Affiliation(s)
- Jane Ru Choi
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia. and The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
| | - Jie Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
| | - Yan Gong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
| | - Shangsheng Feng
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China. and MOE Key Laboratory for Multifunctional Materials and Structures (LMMS), School of Aerospace, Xi'an Jiaotong University, Xi'an, PR China and State Key Laboratory of Mechanical Structure Strength and Vibration, School of Aerospace, Xi'an Jiaotong University, Xi'an, PR China
| | - Wan Abu Bakar Wan Abas
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Belinda Pingguan-Murphy
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China and Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
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20
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Zhao G, Wang H, Hou P, He C, He H. Rapid visual detection of Mycobacterium avium subsp. paratuberculosis by recombinase polymerase amplification combined with a lateral flow dipstick. J Vet Sci 2018; 19:242-250. [PMID: 29284204 PMCID: PMC5879072 DOI: 10.4142/jvs.2018.19.2.242] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/20/2017] [Accepted: 11/24/2017] [Indexed: 02/01/2023] Open
Abstract
Paratuberculosis (Johne's disease) is a chronic debilitating disease of domestic and wild ruminants. However, widespread point-of-care testing is infrequent due to the lack of a robust method. The isothermal recombinase polymerase amplification (RPA) technique has applied for rapid diagnosis. Herein, RPA combined with a lateral flow dipstick (LFD) assay was developed to estimate DNA from Mycobacterium avium subsp. paratuberculosis. First, analytical specificity and sensitivity of the RPA-nfo primer and probe sets were assessed. The assay successfully detected M. paratuberculosis DNA in 30 min at 39℃ with a detection limit of up to eight copies per reaction, which was equivalent to that of the real-time quantitative polymerase chain reaction (qPCR) assay. The assay was specific, as it did not amplify genomes from five other Mycobacterium spp. or five pathogenic enteric bacteria. Six hundred-twelve clinical samples (320 fecal and 292 serum) were assessed by RPA-LFD, qPCR, and enzyme-linked immunosorbent assay, respectively. The RPA-LFD assay yielded 100% sensitivity, 97.63% specificity, and 98.44% concordance rate with the qPCR results. This is the first report utilizing an RPA-LFD assay to visualize and rapidly detect M. paratuberculosis. Our results show this assay should be a useful method for the diagnosis of paratuberculosis in resource-constrained settings.
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Affiliation(s)
- Guimin Zhao
- Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, Jinan 250014, China.,Ruminant Disease Research Center, Shandong Normal University, Jinan 250014, China
| | - Hongmei Wang
- Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, Jinan 250014, China.,Ruminant Disease Research Center, Shandong Normal University, Jinan 250014, China
| | - Peili Hou
- Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, Jinan 250014, China.,Ruminant Disease Research Center, Shandong Normal University, Jinan 250014, China
| | - Chengqiang He
- Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, Jinan 250014, China.,Ruminant Disease Research Center, Shandong Normal University, Jinan 250014, China
| | - Hongbin He
- Key Laboratory of Animal Resistant Biology of Shandong, College of Life Science, Shandong Normal University, Jinan 250014, China.,Ruminant Disease Research Center, Shandong Normal University, Jinan 250014, China
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21
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Qian W, Lu Y, Meng Y, Ye Z, Wang L, Wang R, Zheng Q, Wu H, Wu J. Field Detection of Citrus Huanglongbing Associated with ' Candidatus Liberibacter Asiaticus' by Recombinese Polymerase Amplification within 15 min. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:5473-5480. [PMID: 29781618 DOI: 10.1021/acs.jafc.8b01015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
' Candidatus Liberibacter asiaticus' (Las) is the most prevalent bacterium associated with huanglongbing, which is one of the most destructive diseases of citrus. In this paper, an extremely rapid and simple method for field detection of Las from leaf samples, based on recombinase polymerase amplification (RPA), is described. Three RPA primer pairs were designed and evaluated. RPA amplification was optimized so that it could be accomplished within 10 min. In combination with DNA crude extraction by a 50-fold dilution after 1 min of grinding in 0.5 M sodium hydroxide and visual detection via fluorescent DNA dye (positive samples display obvious green fluorescence while negative samples remain colorless), the whole detection process can be accomplished within 15 min. The sensitivity and specificity of this RPA-based method were evaluated and were proven to be equal to those of real-time PCR. The reliability of this method was also verified by analyzing field samples.
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Affiliation(s)
- Wenjuan Qian
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
| | - Ying Lu
- Zhejiang Plant Protection and Quarantine Bureau, Hangzhou 310020 , China
| | - Youqing Meng
- Zhejiang Plant Protection and Quarantine Bureau, Hangzhou 310020 , China
| | - Zunzhong Ye
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
| | - Liu Wang
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
| | - Rui Wang
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
| | - Qiqi Zheng
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
| | - Hui Wu
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
| | - Jian Wu
- College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou 310058 , China
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22
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Castellanos-Gonzalez A, White A, Melby P, Travi B. Molecular diagnosis of protozoan parasites by Recombinase Polymerase Amplification. Acta Trop 2018; 182:4-11. [PMID: 29452112 DOI: 10.1016/j.actatropica.2018.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/08/2018] [Accepted: 02/11/2018] [Indexed: 12/29/2022]
Abstract
Infections caused by protozoan parasites affect millions of people around the world. Traditionally, diagnosis was made by microscopy, which is insensitive and in some cases not specific. Molecular methods are highly sensitive and specific, but equipment costs and personnel training limit its availability only to specialized centers, usually far from populations with the highest risk of infection. Inexpensive methods that can be applied at the point of care (POC), especially in places with limited health infrastructure, would be a major advantage. Isothermal amplification of nucleic acids does not require thermocyclers and is relatively inexpensive and easy to implement. Among isothermal methods, recombinase polymerase amplification (RPA) is sensitive and potentially applicable at POC. We and others have developed RPA diagnostic tests to detect protozoan parasites of medical importance. Overall, our results have shown high specificity with limits of detection similar to PCR. Currently, the optimization of RPA for use at the POC is under development, and in the near future the tests should become available to detect protozoan infections in the field. In this review we discuss the current status, challenges, and future of RPA in the field of molecular diagnosis of protozoan parasites.
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23
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Diéguez L, Winter M, Molan S, Monis P, King B, Thierry B. Disposable microfluidic micromixers for effective capture of Cryptosporidium parvum oocysts from water samples. J Biol Eng 2018; 12:4. [PMID: 29599821 PMCID: PMC5870503 DOI: 10.1186/s13036-018-0095-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/14/2018] [Indexed: 01/08/2023] Open
Abstract
Background Protecting drinking water supplies from pathogens such as Cryptosporidium parvum is a major concern for water utilities worldwide. The sensitivity and specificity of current detection methods are largely determined by the effectiveness of the concentration and separation methods used. The purpose of this study is to develop micromixers able to specifically isolate and concentrate Cryptosporidium, while allowing in situ analysis. Results In this study, disposable microfluidic micromixers were fabricated to effectively isolate Cryptosporidium parvum oocysts from water samples, while allowing direct observation and enabling quantification of oocysts captured in the device using high quality immunofluorescence microscopy. In parallel, quantitative analysis of the capture yield was carried out by analyzing the waste from the microfluidics outlet with an Imaging Flow Cytometer. At the optimal flow rate, capture efficiencies up to 96% were achieved in spiked samples. Conclusions Scaled microfluidic isolation and detection of Cryptosporidium parvum will provide a faster and more efficient detection method for Cryptosporidium compared to other available laboratory-scale technologies.
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Affiliation(s)
- L Diéguez
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia.,2International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - M Winter
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia
| | - S Molan
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia
| | - P Monis
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia.,3South Australian Water Corporation, Adelaide, SA Australia
| | - B King
- 3South Australian Water Corporation, Adelaide, SA Australia
| | - B Thierry
- 1Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia Australia
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24
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Mayboroda O, Katakis I, O'Sullivan CK. Multiplexed isothermal nucleic acid amplification. Anal Biochem 2018; 545:20-30. [PMID: 29353064 DOI: 10.1016/j.ab.2018.01.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/14/2022]
Abstract
Multiplexed isothermal amplification and detection of nucleic acid sequences and biomarkers is of increasing importance in diverse areas including advanced diagnostics, food quality control and environmental monitoring. Whilst there are several very elegant isothermal amplification approaches, multiplexed amplification remains a challenge, requiring careful experimental design and optimisation, from judicious primer design in order to avoid the formation of primer dimers and non-specific amplification, applied temperature as well as the ratio and concentration of primers. In this review, we describe the various approaches that have been reported to date for multiplexed isothermal amplification, for both "one-pot" multiplexing as well as parallelised multiplexing using loop-mediated isothermal amplification, strand-displacement amplification, helicase-dependent amplification, rolling circle amplification, nucleic acid sequence-based amplification, with a particular focus on recombinase polymerase amplification.
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Affiliation(s)
- Olena Mayboroda
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ioanis Katakis
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain.
| | - Ciara K O'Sullivan
- Interfibio Research Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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25
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Raja B, Goux HJ, Marapadaga A, Rajagopalan S, Kourentzi K, Willson RC. Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens. J Appl Microbiol 2017; 123:544-555. [PMID: 28510991 DOI: 10.1111/jam.13493] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 01/17/2017] [Accepted: 04/20/2017] [Indexed: 01/19/2023]
Abstract
AIMS To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens. METHODS AND RESULTS The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection. CONCLUSIONS The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established. SIGNIFICANCE AND IMPACT OF THE STUDY Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens.
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Affiliation(s)
- B Raja
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - H J Goux
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - A Marapadaga
- Medical Center Laboratories, Houston, TX, USA.,De Novo Diagnostics, Houston, TX, USA
| | - S Rajagopalan
- Medical Center Laboratories, Houston, TX, USA.,De Novo Diagnostics, Houston, TX, USA
| | - K Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - R C Willson
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.,Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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26
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Abstract
Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37-42°C, with minimal sample preparation and capable of amplifying as low as 1-10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.
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Affiliation(s)
- Ivan Magriñá Lobato
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain
| | - Ciara K O'Sullivan
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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27
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Advances and challenges of fully integrated paper-based point-of-care nucleic acid testing. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.05.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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28
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Ryan U, Paparini A, Oskam C. New Technologies for Detection of Enteric Parasites. Trends Parasitol 2017; 33:532-546. [DOI: 10.1016/j.pt.2017.03.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 12/21/2022]
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29
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Wang R, Zhang F, Wang L, Qian W, Qian C, Wu J, Ying Y. Instant, Visual, and Instrument-Free Method for On-Site Screening of GTS 40-3-2 Soybean Based on Body-Heat Triggered Recombinase Polymerase Amplification. Anal Chem 2017; 89:4413-4418. [PMID: 28345860 DOI: 10.1021/acs.analchem.7b00964] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
On-site monitoring the plantation of genetically modified (GM) crops is of critical importance in agriculture industry throughout the world. In this paper, a simple, visual and instrument-free method for instant on-site detection of GTS 40-3-2 soybean has been developed. It is based on body-heat recombinase polymerase amplification (RPA) and followed with naked-eye detection via fluorescent DNA dye. Combining with extremely simplified sample preparation, the whole detection process can be accomplished within 10 min and the fluorescent results can be photographed by an accompanied smart phone. Results demonstrated a 100% detection rate for screening of practical GTS 40-3-2 soybean samples by 20 volunteers under different ambient temperatures. This method is not only suitable for on-site detection of GM crops but also demonstrates great potential to be applied in other fields.
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Affiliation(s)
- Rui Wang
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou, 310058, China
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University , Fuzhou, 350108, China
| | - Liu Wang
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou, 310058, China
| | - Wenjuan Qian
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou, 310058, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou, 310058, China
| | - Yibin Ying
- College of Biosystems Engineering and Food Science, Zhejiang University , Hangzhou, 310058, China
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30
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del Río JS, Lobato IM, Mayboroda O, Katakis I, O’Sullivan CK. Enhanced solid-phase recombinase polymerase amplification and electrochemical detection. Anal Bioanal Chem 2017; 409:3261-3269. [DOI: 10.1007/s00216-017-0269-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/01/2017] [Accepted: 02/20/2017] [Indexed: 11/28/2022]
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31
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Rapid diagnosis of Theileria annulata by recombinase polymerase amplification combined with a lateral flow strip (LF-RPA) in epidemic regions. Vet Parasitol 2017; 237:125-129. [PMID: 28249769 DOI: 10.1016/j.vetpar.2017.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/14/2017] [Accepted: 02/18/2017] [Indexed: 11/20/2022]
Abstract
Rapid and accurate diagnosis of Theileria annulata infection contributes to the formulation of strategies to eradicate this parasite. A simple and efficient diagnostic tool, recombinase polymerase amplification (RPA) combined with a lateral flow (LF) strip, was used in detection of Theileria and compared to other methods that require expensive instruments and skilled personnel. Herein, we established and optimized an LF-RPA method to detect the cytochrome b gene of T. annulata mitochondrial DNA from experimentally infected and field-collected blood samples. This method has many unparalleled characteristics, including that it is rapid (clear detection in 5min at constant temperature), sensitive (the limitation of detection is at least 2pg genomic DNA), and specific (no cross-reaction with other piroplasms that infect cattle). The LF-RPA assay was evaluated via testing 17 field blood samples and comparing the results of that of a PCR, showing 100% agreement, which demonstrates the ability of the LF-RPA assay to detect T. annulata infections in small number of samples (n=17). Taken together, the results indicate that this method could be used as an ideal diagnostic tool for detecting T. annulata in endemic regions with limited to fewer and local resources and could also be a potential technique for the surveillance and control of blood protozoa.
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Gao W, Huang H, Zhang Y, Zhu P, Yan X, Fan J, Chen X. Recombinase Polymerase Amplification-Based Assay for Rapid Detection of Listeria monocytogenes in Food Samples. FOOD ANAL METHOD 2016. [DOI: 10.1007/s12161-016-0775-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Ultrasensitive, rapid and inexpensive detection of DNA using paper based lateral flow assay. Sci Rep 2016; 6:37732. [PMID: 27886248 PMCID: PMC5123575 DOI: 10.1038/srep37732] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/31/2016] [Indexed: 01/07/2023] Open
Abstract
Sensitive, specific, rapid, inexpensive and easy-to-use nucleic acid tests for use at the point-of-need are critical for the emerging field of personalised medicine for which companion diagnostics are essential, as well as for application in low resource settings. Here we report on the development of a point-of-care nucleic acid lateral flow test for the direct detection of isothermally amplified DNA. The recombinase polymerase amplification method is modified slightly to use tailed primers, resulting in an amplicon with a duplex flanked by two single stranded DNA tails. This tailed amplicon facilitates detection via hybridisation to a surface immobilised oligonucleotide capture probe and a gold nanoparticle labelled reporter probe. A detection limit of 1 × 10-11 M (190 amol), equivalent to 8.67 × 105 copies of DNA was achieved, with the entire assay, both amplification and detection, being completed in less than 15 minutes at a constant temperature of 37 °C. The use of the tailed primers obviates the need for hapten labelling and consequent use of capture and reporter antibodies, whilst also avoiding the need for any post-amplification processing for the generation of single stranded DNA, thus presenting an assay that can facilely find application at the point of need.
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34
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Chu C, Ge S, Zhang J, Lin H, Liu G, Chen X. Enzyme-free colorimetric determination of EV71 virus using a 3D-MnO 2-PEG nanoflower and 4-MBA-MA-AgNPs. NANOSCALE 2016; 8:16168-16171. [PMID: 27714132 DOI: 10.1039/c6nr06005f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We present a simple colorimetric assay for EV71 virus detection based on the aggregation of 4-mercaptobenzoic acid (4-MBA) and melamine (MA) modified silver nanoparticles (4-MBA-MA-AgNPs) in the presence of Mn2+. The EV71-Ab1 was incubated on a 96-well plate and the EV71-Ab2 was labeled on the surface of three-dimensional nanoflower-like MnO2-PEG (3D-MnO2-PEG). After layer-by-layer immunoreactions, the EV71 virus and the corresponding 3D-MnO2-PEG-Ab2 were captured on the plate. With the addition of Vitamin C (Vc), Mn2+ was released from the 3D-MnO2-PEG and then the aggregation of the 4-MBA-MA-AgNPs was induced, allowing a naked-eye detection limit of EV71 virus to be as low as 5 × 104 particles per mL, which is about three orders of magnitude lower than the conventional enzyme-linked immunosorbent assay (ELISA). This enzyme-free immunoassay based on a hybrid 3D-MnO2 features signal amplification strategies via a simple reduction reaction.
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Affiliation(s)
- Chengchao Chu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University, Xiamen 361102, China.
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University, Xiamen 361102, China. and National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jing Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University, Xiamen 361102, China. and National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Huirong Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University, Xiamen 361102, China.
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics & Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University, Xiamen 361102, China.
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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35
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A Novel Isothermal Assay of Borrelia burgdorferi by Recombinase Polymerase Amplification with Lateral Flow Detection. Int J Mol Sci 2016; 17:ijms17081250. [PMID: 27527151 PMCID: PMC5000648 DOI: 10.3390/ijms17081250] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 11/24/2022] Open
Abstract
A novel isothermal detection for recombinase polymerase amplification with lateral flow (LF-RPA) was established for Borrelia burgdorferi (B. burgdorferi) detection in this study. This assay with high sensitivity and specificity can get a visible result without any additional equipment in 30 min. We designed a pair of primers according to recA gene of B. burgdorferi strains and a methodology evaluation was performed. The results showed that the RPA assay based on the recA gene was successfully applied in B. burgdorferi detection, and its specific amplification was only achieved from the genomic DNA of B. burgdorferi. The detection limit of the new assay was about 25 copies of the B. burgdorferi genomic DNA. Twenty Lyme borreliosis patients’ serum samples were detected by LF-RPA assay, real-time qPCR and nested-PCR. Results showed the LF-RPA assay is more effective than nested-PCR for its shorter reaction time and considerably higher detection rate. This method is of great value in clinical rapid detection for Lyme borreliosis. Using the RPA assay might be a megatrend for DNA detection in clinics and endemic regions.
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36
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Wu YD, Zhou DH, Zhang LX, Zheng WB, Ma JG, Wang M, Zhu XQ, Xu MJ. Recombinase polymerase amplification (RPA) combined with lateral flow (LF) strip for equipment-free detection of Cryptosporidium spp. oocysts in dairy cattle feces. Parasitol Res 2016; 115:3551-5. [DOI: 10.1007/s00436-016-5120-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/04/2016] [Indexed: 01/31/2023]
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37
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Daher RK, Stewart G, Boissinot M, Bergeron MG. Recombinase Polymerase Amplification for Diagnostic Applications. Clin Chem 2016; 62:947-58. [PMID: 27160000 PMCID: PMC7108464 DOI: 10.1373/clinchem.2015.245829] [Citation(s) in RCA: 380] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/15/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND First introduced in 2006, recombinase polymerase amplification (RPA) has stirred great interest, as evidenced by 75 publications as of October 2015, with 56 of them just in the last 2 years. The widespread adoption of this isothermal molecular tool in many diagnostic fields represents an affordable (approximately 4.3 USD per test), simple (few and easy hands-on steps), fast (results within 5–20 min), and sensitive (single target copy number detected) method for the identification of pathogens and the detection of single nucleotide polymorphisms in human cancers and genetically modified organisms. CONTENT This review summarizes the current knowledge on RPA. The molecular diagnostics of various RNA/DNA pathogens is discussed while highlighting recent applications in clinical settings with focus on point-of-care (POC) bioassays and on automated fluidic platforms. The strengths and limitations of this isothermal method are also addressed. SUMMARY RPA is becoming a molecular tool of choice for the rapid, specific, and cost-effective identification of pathogens. Owing to minimal sample-preparation requirements, low operation temperature (25–42 °C), and commercial availability of freeze-dried reagents, this method has been applied outside laboratory settings, in remote areas, and interestingly, onboard automated sample-to-answer microfluidic devices. RPA is undoubtedly a promising isothermal molecular technique for clinical microbiology laboratories and emergence response in clinical settings.
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Affiliation(s)
- Rana K Daher
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City (Québec), Canada
| | - Gale Stewart
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada
| | - Maurice Boissinot
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada
| | - Michel G Bergeron
- Centre de recherche en infectiologie de l'Université Laval (CRI), Axe maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City (Québec), Canada.
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38
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Hui W, Zhang S, Zhang C, Wan Y, Zhu J, Zhao G, Wu S, Xi D, Zhang Q, Li N, Cui Y. A novel lateral flow assay based on GoldMag nanoparticles and its clinical applications for genotyping of MTHFR C677T polymorphisms. NANOSCALE 2016; 8:3579-3587. [PMID: 26804455 DOI: 10.1039/c5nr07547e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Current techniques for single nucleotide polymorphism (SNP) detection require tedious experimental procedures and expensive and sophisticated instruments. In this study, a visual genotyping method has been successfully established via combining ARMS-PCR with gold magnetic nanoparticle (GoldMag)-based lateral flow assay (LFA) and applied to the genotyping of methylenetetrahydrofolate reductase (MTHFR) C677T. C677T substitution of the gene MTHFR leads to an increased risk of diseases. The genotyping result is easily achievable by visual observation within 5 minutes after loading of the PCR products onto the LFA device. The system is able to accurately assess a broad detection range of initial starting genomic DNA amounts from 5 ng to 1200 ng per test sample. The limit of detection reaches 5 ng. Furthermore, our PCR-LFA system was applied to clinical trials for screening 1721 individuals for the C677T genotypes. The concordance rate of the genotyping results detected by PCR-LFA was up to 99.6% when compared with the sequencing results. Collectively, our PCR-LFA has been proven to be rapid, accurate, sensitive, and inexpensive. This new method is highly applicable for C677T SNP screening in laboratories and clinical practices. More promisingly, it could also be extended to the detection of SNPs of other genes.
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Affiliation(s)
- Wenli Hui
- College of Life Sciences, Northwest University, Xi'an, 710069, China.
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39
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Crannell Z, Castellanos-Gonzalez A, Nair G, Mejia R, White AC, Richards-Kortum R. Multiplexed Recombinase Polymerase Amplification Assay To Detect Intestinal Protozoa. Anal Chem 2016; 88:1610-6. [PMID: 26669715 DOI: 10.1021/acs.analchem.5b03267] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This work describes a proof-of-concept multiplex recombinase polymerase amplification (RPA) assay with lateral flow readout that is capable of simultaneously detecting and differentiating DNA from any of the diarrhea-causing protozoa Giardia, Cryptosporidium, and Entamoeba. Together, these parasites contribute significantly to the global burden of diarrheal illness. Differential diagnosis of these parasites is traditionally accomplished via stool microscopy. However, microscopy is insensitive and can miss up to half of all cases. DNA-based diagnostics such as polymerase chain reaction (PCR) are far more sensitive; however, they rely on expensive thermal cycling equipment, limiting their availability to centralized reference laboratories. Isothermal DNA amplification platforms, such as the RPA platform used in this study, alleviate the need for thermal cycling equipment and have the potential to broaden access to more sensitive diagnostics. Until now, multiplex RPA assays have not been developed that are capable of simultaneously detecting and differentiating infections caused by different pathogens. We developed a multiplex RPA assay to detect the presence of DNA from Giardia, Cryptosporidium, and Entamoeba. The multiplex assay was characterized using synthetic DNA, where the limits-of-detection were calculated to be 403, 425, and 368 gene copies per reaction of the synthetic Giardia, Cryptosporidium, and Entamoeba targets, respectively (roughly 1.5 orders of magnitude higher than for the same targets in a singleplex RPA assay). The multiplex assay was also characterized using DNA extracted from live parasites spiked into stool samples where the limits-of-detection were calculated to be 444, 6, and 9 parasites per reaction for Giardia, Cryptosporidium, and Entamoeba parasites, respectively. This proof-of-concept assay may be reconfigured to detect a wide variety of targets by re-designing the primer and probe sequences.
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Affiliation(s)
- Zachary Crannell
- 1980 West Getaway Trail, Flagstaff, Arizona 86005, United States.,Department of Internal Medicine, University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555.0435, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Department of Pediatrics, Section of Tropical Medicine; Department of Medicine, Section of Infectious Diseases; and National School of Tropical Medicine, Baylor College of Medicine 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , Mary Moody Northen, Room 4.230, 301 University Boulevard, Galveston, Texas 77555-0435, United States
| | - Alejandro Castellanos-Gonzalez
- 1980 West Getaway Trail, Flagstaff, Arizona 86005, United States.,Department of Internal Medicine, University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555.0435, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Department of Pediatrics, Section of Tropical Medicine; Department of Medicine, Section of Infectious Diseases; and National School of Tropical Medicine, Baylor College of Medicine 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , Mary Moody Northen, Room 4.230, 301 University Boulevard, Galveston, Texas 77555-0435, United States
| | - Gayatri Nair
- 1980 West Getaway Trail, Flagstaff, Arizona 86005, United States.,Department of Internal Medicine, University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555.0435, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Department of Pediatrics, Section of Tropical Medicine; Department of Medicine, Section of Infectious Diseases; and National School of Tropical Medicine, Baylor College of Medicine 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , Mary Moody Northen, Room 4.230, 301 University Boulevard, Galveston, Texas 77555-0435, United States
| | - Rojelio Mejia
- 1980 West Getaway Trail, Flagstaff, Arizona 86005, United States.,Department of Internal Medicine, University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555.0435, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Department of Pediatrics, Section of Tropical Medicine; Department of Medicine, Section of Infectious Diseases; and National School of Tropical Medicine, Baylor College of Medicine 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , Mary Moody Northen, Room 4.230, 301 University Boulevard, Galveston, Texas 77555-0435, United States
| | - A Clinton White
- 1980 West Getaway Trail, Flagstaff, Arizona 86005, United States.,Department of Internal Medicine, University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555.0435, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Department of Pediatrics, Section of Tropical Medicine; Department of Medicine, Section of Infectious Diseases; and National School of Tropical Medicine, Baylor College of Medicine 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , Mary Moody Northen, Room 4.230, 301 University Boulevard, Galveston, Texas 77555-0435, United States
| | - Rebecca Richards-Kortum
- Department of Bioengineering, Rice University , Houston, Texas 77030, United States.,1980 West Getaway Trail, Flagstaff, Arizona 86005, United States.,Department of Internal Medicine, University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555.0435, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Department of Pediatrics, Section of Tropical Medicine; Department of Medicine, Section of Infectious Diseases; and National School of Tropical Medicine, Baylor College of Medicine 1709 Dryden Road, No. 1700, Houston, Texas 77030, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch , Mary Moody Northen, Room 4.230, 301 University Boulevard, Galveston, Texas 77555-0435, United States
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Fu X, Cheng Z, Yu J, Choo P, Chen L, Choo J. A SERS-based lateral flow assay biosensor for highly sensitive detection of HIV-1 DNA. Biosens Bioelectron 2015; 78:530-537. [PMID: 26669705 DOI: 10.1016/j.bios.2015.11.099] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/29/2015] [Accepted: 11/30/2015] [Indexed: 11/26/2022]
Abstract
User-friendly lateral flow (LF) strips have been extensively used for point-of-care (POC) self-diagnostics, but they have some limitations in their detection sensitivity and quantitative analysis because they only identify the high cut-off value of a biomarker by utilizing color changes that are detected with the naked eye. To resolve these problems associated with LF strips, we developed a novel surface-enhanced Raman scattering (SERS)-based LF assay for the quantitative analysis of a specific biomarker in the low concentration range. Herein, human immunodeficiency virus type 1 (HIV-1) DNA was chosen as the specific biomarker. Raman reporter-labeled gold nanoparticles (AuNPs) were employed as SERS nano tags for targeting and detecting the HIV-1 DNA marker, as opposed to using bare AuNPs in LF strips. It was possible to quantitatively analyze HIV-1 DNA with high sensitivity by monitoring the characteristic Raman peak intensity of the DNA-conjugated AuNPs. Under optimized conditions, the detection limit of our SERS-based lateral flow assay was 0.24 pg/mL, which was at least 1000 times more sensitive compared to colorimetric or fluorescent detection methods. These results demonstrate the potential feasibility of the proposed SERS-based lateral flow assay to quantitatively detect a broad range of genetic diseases with high sensitivity.
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Affiliation(s)
- Xiuli Fu
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | - Ziyi Cheng
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | - Jimin Yu
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | - Priscilla Choo
- Department of Chemistry, Indiana University, Bloomington, IN 47405-102, USA
| | - Lingxin Chen
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea.
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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James A, Macdonald J. Recombinase polymerase amplification: Emergence as a critical molecular technology for rapid, low-resource diagnostics. Expert Rev Mol Diagn 2015; 15:1475-89. [PMID: 26517245 DOI: 10.1586/14737159.2015.1090877] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Isothermal molecular diagnostics are bridging the technology gap between traditional diagnostics and polymerase chain reaction-based methods. These new techniques enable timely and accurate testing, especially in settings where there is a lack of infrastructure to support polymerase chain reaction facilities. Despite this, there is a significant lack of uptake of these technologies in developing countries where they are highly needed. Among these novel isothermal technologies, recombinase polymerase amplification (RPA) holds particular potential for use in developing countries. This rapid nucleic acid amplification approach is fast, highly sensitive and specific, and amenable to countries with a high burden of infectious diseases. Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings. This review focuses on approaching diagnosis of infectious disease with RPA.
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Affiliation(s)
- Ameh James
- a 1 Genecology Research Centre, Inflammation and Healing Research Cluster, School of Science and Engineering, University of the Sunshine Coast , Queensland, Australia.,b 2 Keystone Laboratories International, Kuje, FCT , Abuja, Nigeria
| | - Joanne Macdonald
- a 1 Genecology Research Centre, Inflammation and Healing Research Cluster, School of Science and Engineering, University of the Sunshine Coast , Queensland, Australia.,c 3 Division of Experimental Therapeutics, Department of Medicine, Columbia University , NY, USA
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Castellanos-Gonzalez A, Saldarriaga OA, Tartaglino L, Gacek R, Temple E, Sparks H, Melby PC, Travi BL. A Novel Molecular Test to Diagnose Canine Visceral Leishmaniasis at the Point of Care. Am J Trop Med Hyg 2015; 93:970-5. [PMID: 26240156 DOI: 10.4269/ajtmh.15-0145] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/23/2015] [Indexed: 12/17/2022] Open
Abstract
Dogs are the principal reservoir hosts of zoonotic visceral leishmaniasis (VL) but current serological methods are not sensitive enough to detect all subclinically infected animals, which is crucial to VL control programs. Polymerase chain reaction (PCR) methods have greater sensitivity but require expensive equipment and trained personnel, impairing its implementation in endemic areas. We developed a diagnostic test that uses isothermal recombinase polymerase amplification (RPA) to detect Leishmania infantum. This method was coupled with lateral flow (LF) reading with the naked eye to be adapted as a point-of-care test. The L. infantum RPA-LF had an analytical sensitivity similar to real time-PCR, detecting DNA of 0.1 parasites spiked in dog blood, which was equivalent to 40 parasites/mL. There was no cross amplification with dog or human DNA or with Leishmania braziliensis, Leishmania amazonensis, or Trypanosoma cruzi. The test also amplified Leishmania donovani strains (N = 7). In a group of clinically normal dogs (N = 30), RPA-LF detected more subclinical infections than rK39 strip test, a standard serological method (50% versus 13.3% positivity, respectively; P = 0.005). Also, RPA-LF detected L. infantum in noninvasive mucosal samples of dogs with a sensitivity comparable to blood samples. This novel molecular test may have a positive impact in leishmaniasis control programs.
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Affiliation(s)
- Alejandro Castellanos-Gonzalez
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas; Department of Microbiology and Immunology, Center for Tropical Diseases (CTD), University of Texas Medical Branch (UTMB), Galveston, Texas; Secretaria de Calidad de Vida, Municipalidad de Posadas, Misiones, Argentina; Instituto Municipal de Sanidad Animal, Municipalidad de Posadas, Misiones, Argentina; Baylor University, Waco, Texas
| | - Omar A Saldarriaga
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas; Department of Microbiology and Immunology, Center for Tropical Diseases (CTD), University of Texas Medical Branch (UTMB), Galveston, Texas; Secretaria de Calidad de Vida, Municipalidad de Posadas, Misiones, Argentina; Instituto Municipal de Sanidad Animal, Municipalidad de Posadas, Misiones, Argentina; Baylor University, Waco, Texas
| | - Lilian Tartaglino
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas; Department of Microbiology and Immunology, Center for Tropical Diseases (CTD), University of Texas Medical Branch (UTMB), Galveston, Texas; Secretaria de Calidad de Vida, Municipalidad de Posadas, Misiones, Argentina; Instituto Municipal de Sanidad Animal, Municipalidad de Posadas, Misiones, Argentina; Baylor University, Waco, Texas
| | - Rosana Gacek
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas; Department of Microbiology and Immunology, Center for Tropical Diseases (CTD), University of Texas Medical Branch (UTMB), Galveston, Texas; Secretaria de Calidad de Vida, Municipalidad de Posadas, Misiones, Argentina; Instituto Municipal de Sanidad Animal, Municipalidad de Posadas, Misiones, Argentina; Baylor University, Waco, Texas
| | - Elissa Temple
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas; Department of Microbiology and Immunology, Center for Tropical Diseases (CTD), University of Texas Medical Branch (UTMB), Galveston, Texas; Secretaria de Calidad de Vida, Municipalidad de Posadas, Misiones, Argentina; Instituto Municipal de Sanidad Animal, Municipalidad de Posadas, Misiones, Argentina; Baylor University, Waco, Texas
| | - Hayley Sparks
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas; Department of Microbiology and Immunology, Center for Tropical Diseases (CTD), University of Texas Medical Branch (UTMB), Galveston, Texas; Secretaria de Calidad de Vida, Municipalidad de Posadas, Misiones, Argentina; Instituto Municipal de Sanidad Animal, Municipalidad de Posadas, Misiones, Argentina; Baylor University, Waco, Texas
| | - Peter C Melby
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas; Department of Microbiology and Immunology, Center for Tropical Diseases (CTD), University of Texas Medical Branch (UTMB), Galveston, Texas; Secretaria de Calidad de Vida, Municipalidad de Posadas, Misiones, Argentina; Instituto Municipal de Sanidad Animal, Municipalidad de Posadas, Misiones, Argentina; Baylor University, Waco, Texas
| | - Bruno L Travi
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas; Department of Microbiology and Immunology, Center for Tropical Diseases (CTD), University of Texas Medical Branch (UTMB), Galveston, Texas; Secretaria de Calidad de Vida, Municipalidad de Posadas, Misiones, Argentina; Instituto Municipal de Sanidad Animal, Municipalidad de Posadas, Misiones, Argentina; Baylor University, Waco, Texas
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Development of Recombinase Polymerase Amplification Assays for Detection of Orientia tsutsugamushi or Rickettsia typhi. PLoS Negl Trop Dis 2015; 9:e0003884. [PMID: 26161793 PMCID: PMC4498641 DOI: 10.1371/journal.pntd.0003884] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 06/09/2015] [Indexed: 01/04/2023] Open
Abstract
Sensitive, specific and rapid diagnostic tests for the detection of Orientia tsutsugamushi (O. tsutsugamushi) and Rickettsia typhi (R. typhi), the causative agents of scrub typhus and murine typhus, respectively, are necessary to accurately and promptly diagnose patients and ensure that they receive proper treatment. Recombinase polymerase amplification (RPA) assays using a lateral flow test (RPA-nfo) and real-time fluorescent detection (RPA-exo) were developed targeting the 47-kDa gene of O. tsutsugamushi or 17 kDa gene of R. typhi. The RPA assay was capable of detecting O. tsutsugamushi or R. typhi at levels comparable to that of the quantitative PCR method. Both the RPA-nfo and RPA-exo methods performed similarly with regards to sensitivity when detecting the 17 kDa gene of R. typhi. On the contrary, RPA-exo performed better than RPA-nfo in detecting the 47 kDa gene of O. tsutsugamushi. The clinical performance of the O. tsutsugamushi RPA assay was evaluated using either human patient samples or infected mouse samples. Eight out of ten PCR confirmed positives were determined positive by RPA, and all PCR confirmed negative samples were negative by RPA. Similar results were obtained for R. typhi spiked patient sera. The assays were able to differentiate O. tsutsugamushi and R. typhi from other phylogenetically related bacteria as well as mouse and human DNA. Furthermore, the RPA-nfo reaction was completed in 20 minutes at 37oC followed by a 10 minute incubation at room temperature for development of an immunochromatographic strip. The RPA-exo reaction was completed in 20 minutes at 39oC. The implementation of a cross contamination proof cassette to detect the RPA-nfo fluorescent amplicons provided an alternative to regular lateral flow detection strips, which are more prone to cross contamination. The RPA assays provide a highly time-efficient, sensitive and specific alternative to other methods for diagnosing scrub typhus or murine typhus. Historically, rickettsial pathogens are among the leading causes of morbidity and mortality during military operations. Rickettsial diseases, lately, are reemerging in areas of known abundance or emerging in areas of unknown existence, posing a significant medical concern for local residents and travelers. The diseases are difficult to diagnose as they often share similar symptoms with many other diseases in the same geographical areas. Therefore, it is particularly challenging for clinicians to provide a timely and accurate diagnosis. A recombinase polymerase amplification (RPA)-based nucleic acid detection platform has been used to develop accurate, sensitive, specific, and easy-to-perform assays to detect O. tsutsugamushi or R. typhi, indicative of scrub typhus or murine typhus, respectively. These RPA assays provide similar limits of detection and specificity to that of qPCR. Unlike qPCR, they require no thermocycler and provide multiple end-point monitoring options amendable to different laboratory capabilities. This work presents an alternative assay platform for early detection of O. tsutsugamushi or R. typhi infection so that timely treatment can be prescribed in well-equipped laboratories as well as resource limited areas.
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45
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Choi JR, Tang R, Wang S, Wan Abas WAB, Pingguan-Murphy B, Xu F. Paper-based sample-to-answer molecular diagnostic platform for point-of-care diagnostics. Biosens Bioelectron 2015; 74:427-39. [PMID: 26164488 DOI: 10.1016/j.bios.2015.06.065] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/15/2015] [Accepted: 06/27/2015] [Indexed: 01/04/2023]
Abstract
Nucleic acid testing (NAT), as a molecular diagnostic technique, including nucleic acid extraction, amplification and detection, plays a fundamental role in medical diagnosis for timely medical treatment. However, current NAT technologies require relatively high-end instrumentation, skilled personnel, and are time-consuming. These drawbacks mean conventional NAT becomes impractical in many resource-limited disease-endemic settings, leading to an urgent need to develop a fast and portable NAT diagnostic tool. Paper-based devices are typically robust, cost-effective and user-friendly, holding a great potential for NAT at the point of care. In view of the escalating demand for the low cost diagnostic devices, we highlight the beneficial use of paper as a platform for NAT, the current state of its development, and the existing challenges preventing its widespread use. We suggest a strategy involving integrating all three steps of NAT into one single paper-based sample-to-answer diagnostic device for rapid medical diagnostics in the near future.
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Affiliation(s)
- Jane Ru Choi
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Ruihua Tang
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, PR China; Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, PR China
| | - ShuQi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China; Institute for Translational Medicine, Zhejiang University, Hangzhou, PR China
| | - Wan Abu Bakar Wan Abas
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
| | - Belinda Pingguan-Murphy
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China; The Key Library of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China.
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46
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Nair G, Rebolledo M, White AC, Crannell Z, Richards-Kortum RR, Pinilla AE, Ramírez JD, López MC, Castellanos-Gonzalez A. Detection of Entamoeba histolytica by Recombinase Polymerase Amplification. Am J Trop Med Hyg 2015; 93:591-5. [PMID: 26123960 DOI: 10.4269/ajtmh.15-0276] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/12/2015] [Indexed: 12/24/2022] Open
Abstract
Amebiasis is an important cause of diarrheal disease worldwide and has been associated with childhood malnutrition. Traditional microscopy approaches are neither sensitive nor specific for Entamoeba histolytica. Antigen assays are more specific, but many cases are missed unless tested by molecular methods. Although polymerase chain reaction (PCR) is effective, the need for sophisticated, expensive equipment, infrastructure, and trained personnel limits its usefulness, especially in the resource-limited, endemic areas. Here, we report development of a recombinase polymerase amplification (RPA) method to detect E. histolytica specifically. Using visual detection by lateral flow (LF), the test was highly sensitive and specific and could be performed without additional equipment. The availability of this inexpensive, sensitive, and field-applicable diagnostic test could facilitate rapid diagnosis and treatment of amebiasis in endemic regions.
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Affiliation(s)
- Gayatri Nair
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Mauricio Rebolledo
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
| | - A Clinton White
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Zachary Crannell
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Rebecca Richards-Kortum
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
| | - A Elizabeth Pinilla
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan David Ramírez
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
| | - M Consuelo López
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Alejandro Castellanos-Gonzalez
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas; Department of Bioengineering, Rice University, Houston, Texas; Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia; Departamento de Medicina Interna, Universidad Nacional de Colombia, Bogotá, Colombia; Departamento de Salud Pública, Universidad Nacional de Colombia, Bogotá, Colombia
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47
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Du Y, Hughes RA, Bhadra S, Jiang YS, Ellington AD, Li B. A Sweet Spot for Molecular Diagnostics: Coupling Isothermal Amplification and Strand Exchange Circuits to Glucometers. Sci Rep 2015; 5:11039. [PMID: 26050646 PMCID: PMC4458886 DOI: 10.1038/srep11039] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/30/2015] [Indexed: 12/21/2022] Open
Abstract
Strand exchange nucleic acid circuitry can be used to transduce isothermal nucleic acid amplification products into signals that can be readable on an off-the-shelf glucometer. Loop-mediated isothermal amplification (LAMP) is limited by the accumulation of non-specific products, but nucleic acid circuitry can be used to probe and distinguish specific amplicons. By combining this high temperature isothermal amplification method with a thermostable invertase, we can directly transduce Middle-East respiratory syndrome coronavirus and Zaire Ebolavirus templates into glucose signals, with a sensitivity as low as 20-100 copies/μl, equating to atto-molar (or low zepto-mole). Virus from cell lysates and synthetic templates could be readily amplified and detected even in sputum or saliva. An OR gate that coordinately triggered on viral amplicons further guaranteed fail-safe virus detection. The method describes has potential for accelerating point-of-care applications, in that biological samples could be applied to a transducer that would then directly interface with an off-the-shelf, approved medical device.
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Affiliation(s)
- Yan Du
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Randall A Hughes
- Applied Research Laboratories, The University of Texas at Austin, Austin, TX 78758, USA
| | - Sanchita Bhadra
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Sherry Jiang
- Department of Chemsitry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Bingling Li
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
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48
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Crannell ZA, Rohrman B, Richards-Kortum R. Development of a quantitative recombinase polymerase amplification assay with an internal positive control. J Vis Exp 2015:52620. [PMID: 25867513 PMCID: PMC4401391 DOI: 10.3791/52620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest.
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49
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Chen Y, Xianyu Y, Wang Y, Zhang X, Cha R, Sun J, Jiang X. One-step detection of pathogens and viruses: combining magnetic relaxation switching and magnetic separation. ACS NANO 2015; 9:3184-91. [PMID: 25743636 DOI: 10.1021/acsnano.5b00240] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report a sensing methodology that combines magnetic separation (MS) and magnetic relaxation switching (MS-MRS) for one-step detection of bacteria and viruses with high sensitivity and reproducibility. We first employ a magnetic field of 0.01 T to separate the magnetic beads of large size (250 nm in diameter) from those of small size (30 nm in diameter) and use the transverse relaxation time (T2) of the water molecules around the 30 nm magnetic beads (MB30) as the signal readout of the immunoassay. An MS-MRS sensor integrates target enrichment, extraction, and detection into one step, and the entire immunoassay can be completed within 30 min. Compared with a traditional MRS sensor, an MS-MRS sensor shows enhanced sensitivity, better reproducibility, and convenient operation, thus providing a promising platform for point-of-care testing.
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Affiliation(s)
- Yiping Chen
- †Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Yunlei Xianyu
- †Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Yu Wang
- §Beijing Institute for Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, 95 Yongan Road, Xicheng District, Beijing, 100050, China
| | - Xiaoqing Zhang
- †Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Ruitao Cha
- †Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Jiashu Sun
- †Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Xingyu Jiang
- †Beijing Engineering Research Center for BioNanotechnology and CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, Beijing, 100190, China
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Rohrman B, Richards-Kortum R. Inhibition of recombinase polymerase amplification by background DNA: a lateral flow-based method for enriching target DNA. Anal Chem 2015; 87:1963-7. [PMID: 25560368 DOI: 10.1021/ac504365v] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recombinase polymerase amplification (RPA) may be used to detect a variety of pathogens, often after minimal sample preparation. However, previous work has shown that whole blood inhibits RPA. In this paper, we show that the concentrations of background DNA found in whole blood prevent the amplification of target DNA by RPA. First, using an HIV-1 RPA assay with known concentrations of nonspecific background DNA, we show that RPA tolerates more background DNA when higher HIV-1 target concentrations are present. Then, using three additional assays, we demonstrate that the maximum amount of background DNA that may be tolerated in RPA reactions depends on the DNA sequences used in the assay. We also show that changing the RPA reaction conditions, such as incubation time and primer concentration, has little effect on the ability of RPA to function when high concentrations of background DNA are present. Finally, we develop and characterize a lateral flow-based method for enriching the target DNA concentration relative to the background DNA concentration. This sample processing method enables RPA of 10(4) copies of HIV-1 DNA in a background of 0-14 μg of background DNA. Without lateral flow sample enrichment, the maximum amount of background DNA tolerated is 2 μg when 10(6) copies of HIV-1 DNA are present. This method requires no heating or other external equipment, may be integrated with upstream DNA extraction and purification processes, is compatible with the components of lysed blood, and has the potential to detect HIV-1 DNA in infant whole blood with high proviral loads.
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Affiliation(s)
- Brittany Rohrman
- Department of Bioengineering, Rice University , 6100 Main St MS-142, Houston, Texas 77005, United States
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