251
|
Wu X, Tay JK, Goh CK, Chan C, Lee YH, Springs SL, Wang DY, Loh KS, Lu TK, Yu H. Digital CRISPR-based method for the rapid detection and absolute quantification of nucleic acids. Biomaterials 2021; 274:120876. [PMID: 34034027 DOI: 10.1016/j.biomaterials.2021.120876] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/23/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022]
Abstract
Rapid diagnostics of adventitious agents in biopharmaceutical/cell manufacturing release testing and the fight against viral infection have become critical. Quantitative real-time PCR and CRISPR-based methods rapidly detect DNA/RNA in 1 h but suffer from inter-site variability. Absolute quantification of DNA/RNA by methods such as digital PCR reduce this variability but are currently too slow for wider application. Here, we report a RApid DIgital Crispr Approach (RADICA) for absolute quantification of nucleic acids in 40-60 min. Using SARS-CoV-2 as a proof-of-concept target, RADICA allows for absolute quantification with a linear dynamic range of 0.6-2027 copies/μL (R2 value > 0.99), high accuracy and low variability, no cross-reactivity to similar targets, and high tolerance to human background DNA. RADICA's versatility is validated against other targets such as Epstein-Barr virus (EBV) from human B cells and patients' serum. RADICA can accurately detect and absolutely quantify EBV DNA with similar dynamic range of 0.5-2100 copies/μL (R2 value > 0.98) in 1 h without thermal cycling, providing a 4-fold faster alternative to digital PCR-based detection. RADICA therefore enables rapid and sensitive absolute quantification of nucleic acids which can be widely applied across clinical, research, and biomanufacturing areas.
Collapse
Affiliation(s)
- Xiaolin Wu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Joshua K Tay
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Chuan Keng Goh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Cheryl Chan
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Yie Hou Lee
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Stacy L Springs
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - De Yun Wang
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Kwok Seng Loh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Timothy K Lu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA.
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Institute of Bioengineering and Bioimaging, A*STAR, The Nanos, #04-01, 31, Biopolis Way, 138669, Singapore; Mechanobiology Institute, National University of Singapore, T-Lab, #05-01, 5A Engineering Drive 1, 117411, Singapore; Department of Physiology & the Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, MD9-04-11, 2 Medical Drive, 117593, Singapore.
| |
Collapse
|
252
|
Fan J, Chen W, Zhang Y, Liu Z, Li X, Ding H, Yi L, Chen J, Zhao M. Development of a reverse-transcription recombinase polymerase amplification assay with a lateral flow assay for rapid detection of avian orthoavulavirus 1. J Vet Diagn Invest 2021; 33:308-312. [PMID: 33685333 DOI: 10.1177/1040638721990122] [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: 11/15/2022] Open
Abstract
Newcastle disease is an avian infectious disease caused by avian orthoavulavirus 1, also known as Newcastle disease virus (NDV). This disease has caused significant economic losses to the poultry industry worldwide. The rapid and simple detection of NDV infection is crucial to inform the appropriate control measures. We developed a reverse-transcription recombinase polymerase amplification (RT-RPA) assay combined with a lateral flow assay (LFA) for NDV detection. The RPA assay can be completed at 37°C within 20 min, and the RPA result can be visualized by the LFA within 5 min. The NDV RT-RPA-LFA detected NDV specifically with no cross-reactivity with other pathogens. The detection limit of NDV cDNA with our RT-RPA-LFA was 3.34 × 10-3 ng/μL. Consequently, the RT-RPA-LFA showed good potential for the detection of NDV infection in the field, especially in resource-limited settings.
Collapse
Affiliation(s)
- Jindai Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yuanyuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhixiang Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaoming Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| |
Collapse
|
253
|
Li X, Zheng T, Xie YN, Li F, Jiang X, Hou X, Wu P. Recombinase Polymerase Amplification Coupled with a Photosensitization Colorimetric Assay for Fast Salmonella spp. Testing. Anal Chem 2021; 93:6559-6566. [PMID: 33852278 DOI: 10.1021/acs.analchem.1c00791] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Salmonella spp. is one of the most serious foodborne pathogens causing millions of infection cases annually, especially in resource-limited areas. The standard culture method (2-3 days) and current nucleic acid amplification-based testing are not suitable for on-site testing in rural areas with heavy Salmonella spp. burden. Here, we developed a colorimetric recombinase polymerase amplification (RPA) method for fast and sensitive Salmonella spp. testing in 1 h. Specifically, the invA gene from the genomic DNA of Salmonella spp. was amplified isothermally to produce double-stranded DNA (dsDNA) amplicons, which were directly quantified by a photosensitization colorimetric assay. The proposed method offered the lowest detectable concentration of 5 × 103 colony-forming units/mL (cfu/mL), which is much lower than that of ELISA (105-107 cfu/mL). The detectable limit could be further pushed down to 3 cfu/mL upon coupling with bacteria pre-enrichment for 6 h. Analysis of synthetic milk samples confirmed the high precision (90%) and specificity (95%) of the method for Salmonella spp. testing. Moreover, use of a DNA releaser could further simplify the whole testing operation. Because RPA features low-temperature amplification (25-42 °C) without the need for specific instruments and the dsDNA-based photosensitization colorimetric assay served as a simple and facile readout for RPA, our method thus allows fast and low-cost Salmonella spp. testing in food samples.
Collapse
Affiliation(s)
- Xianming Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Ting Zheng
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Ya-Ni Xie
- State Key Laboratory of Hydraulics and Mountain River Engineering, Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Feng Li
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xia Jiang
- National Engineering Research Center for Flue Gas Desulfurization, Sichuan University, Chengdu 610064, China
| | - Xiandeng Hou
- State Key Laboratory of Hydraulics and Mountain River Engineering, Analytical & Testing Center, Sichuan University, Chengdu 610064, China.,College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Peng Wu
- State Key Laboratory of Hydraulics and Mountain River Engineering, Analytical & Testing Center, Sichuan University, Chengdu 610064, China.,College of Chemistry, Sichuan University, Chengdu 610064, China
| |
Collapse
|
254
|
Chen K, Ma B, Li J, Chen E, Xu Y, Yu X, Sun C, Zhang M. A Rapid and Sensitive Europium Nanoparticle-Based Lateral Flow Immunoassay Combined with Recombinase Polymerase Amplification for Simultaneous Detection of Three Food-Borne Pathogens. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18094574. [PMID: 33925871 PMCID: PMC8123443 DOI: 10.3390/ijerph18094574] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/25/2022]
Abstract
Food-borne pathogens have become an important public threat to human health. There are many kinds of pathogenic bacteria in food consumed daily. A rapid and sensitive testing method for multiple food-borne pathogens is essential. Europium nanoparticles (EuNPs) are used as fluorescent probes in lateral flow immunoassays (LFIAs) to improve sensitivity. Here, recombinase polymerase amplification (RPA) combined with fluorescent LFIA was established for the simultaneous and quantitative detection of Listeria monocytogenes, Vibrio parahaemolyticus, and Escherichia coliO157:H7. In this work, the entire experimental process could be completed in 20 min at 37 °C. The limits of detection (LODs) of EuNP-based LFIA–RPA were 9.0 colony-forming units (CFU)/mL for Listeria monocytogenes, 7.0 CFU/mL for Vibrio parahaemolyticus, and 4.0 CFU/mL for Escherichia coliO157:H7. No cross-reaction could be observed in 22 bacterial strains. The fluorescent LFIA–RPA assay exhibits high sensitivity and good specificity. Moreover, the average recovery of the three food-borne pathogens spiked in food samples was 90.9–114.2%. The experiments indicate the accuracy and reliability of the multiple fluorescent test strips. Our developed EuNP-based LFIA–RPA assay is a promising analytical tool for the rapid and simultaneous detection of multiple low concentrations of food-borne pathogens.
Collapse
Affiliation(s)
- Kai Chen
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Biao Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Jiali Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Erjing Chen
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Ying Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
| | - Chuanxin Sun
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, EuSwedish University of Agricultural Science (SLU), P.O. Box 7080, SE-75007 Uppsala, Sweden;
| | - Mingzhou Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China; (K.C.); (B.M.); (J.L.); (E.C.); (Y.X.); (X.Y.)
- Correspondence: ; Tel.: +86-571-8691-4476; Fax: +86-571-8691-4510
| |
Collapse
|
255
|
Zhang L, Peng J, Chen J, Xu L, Zhang Y, Li Y, Zhao J, Xiang L, Ge Y, Cheng W. Highly Sensitive Detection of Low-Abundance BRAF V600E Mutation in Fine-Needle Aspiration Samples by Zip Recombinase Polymerase Amplification. Anal Chem 2021; 93:5621-5628. [PMID: 33764743 DOI: 10.1021/acs.analchem.1c00405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Papillary thyroid carcinoma (PTC) is the most common thyroid cancer with high incidence in endocrine tumors, which emphasizes the significance of accurate diagnostics. Still, the commonly used cytological method (fine-needle aspiration (FNA) cytology) and molecular diagnostic methods (such as PCR and sequencing) are limited in terms of diagnostic time, sensitivity, and user-friendliness. In this study, we introduce a novel Zip recombinase polymerase amplification (Z-RPA) strategy to efficiently detect rare mutant alleles in PTC fine-needle aspiration samples, which is sensitive, fast, and simple to manipulate. Using Zip nucleic acid (ZNA) probes to clamp the mutation region, the phi 29 polymerase could selectively displace mismatched ZNA probes and start amplification, while leaving complementary ZNA probes untouched and blocking amplification according to genotype. We demonstrated the good sensitivity and specificity of this strategy with optimized conditions and design, which enabled detection of BRAF V600E mutation in a total 4 ng of genomic DNA within 40 min (≈1 copy). Robust behavior in clinical specimen analysis was also demonstrated. The Z-RPA strategy provides a pragmatic approach to rapidly, sensitively, and easily detect BRAF V600E mutation in clinical fine-needle aspiration samples, which is a promising method for early cancer diagnosis and treatment guideline.
Collapse
Affiliation(s)
- Lutan Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China.,United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen 361000, P. R. China
| | - Jian Peng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Lulu Xu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Yangli Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Ying Li
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Jie Zhao
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Linguo Xiang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Yunsheng Ge
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen 361000, P. R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| |
Collapse
|
256
|
El-Tholoth M, Bai H, Mauk MG, Saif L, Bau HH. A portable, 3D printed, microfluidic device for multiplexed, real time, molecular detection of the porcine epidemic diarrhea virus, transmissible gastroenteritis virus, and porcine deltacoronavirus at the point of need. LAB ON A CHIP 2021; 21:1118-1130. [PMID: 33527920 PMCID: PMC7990716 DOI: 10.1039/d0lc01229g] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV) are emerging/reemerging coronaviruses (CoVs) of neonatal pigs that cause great economic losses to pig farms and pork processors. Specific, rapid, and simple multiplex detection of these viruses is critical to enable prompt implementation of appropriate control measures. Conventional methods for molecular diagnosis require skilled personnel and relatively sophisticated equipment, restricting their use in centralized laboratories. We developed a low-cost, rapid, semi-quantitative, field deployable, 3D-printed microfluidic device for auto-distribution of samples and self-sealing and real-time and reverse transcription-loop-mediated isothermal amplification (RT-LAMP), enabling the co-detection of PEDV, TGEV and PDCoV within 30 minutes. Our assay's analytical performance is comparable with a benchtop, real-time RT-LAMP assay and the gold standard quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay with limits of detection of 10 genomic copies per reaction for PEDV and PDCoV, and 100 genomic copies per reaction for TGEV. Evaluation of clinical specimens from diseased pigs with our microfluidic device revealed excellent concordance with both benchtop RT-LAMP and qRT-PCR. Our portable RT-LAMP microfluidic chip will potentially facilitate simple, specific, rapid multiplexed detection of harmful infections in minimally equipped veterinary diagnostic laboratories and on-site in pigs' farms.
Collapse
Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt.
| | | | | | | | | |
Collapse
|
257
|
Mai HN, Aranguren Caro LF, Cruz-Flores R, Dhar AK. Development of a Recombinase Polymerase Amplification (RPA) assay for acute hepatopancreatic necrosis disease (AHPND) detection in Pacific white shrimp (Penaeus vannamei). Mol Cell Probes 2021; 57:101710. [PMID: 33722662 DOI: 10.1016/j.mcp.2021.101710] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/23/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is currently the most important bacterial disease of shrimp that has caused enormous losses to the shrimp industry worldwide. The causative agent of AHPND are Vibrio spp. Carrying plasmids containing the pirA and pirB genes which encode binary toxins, PirAB. Currently, AHPND is mostly diagnosed by PCR-based platforms which require the use of sophisticated laboratory instrumentation and are not suitable for a point-of-care diagnostics. Therefore, the availability of an alternative method based on isothermal amplification would be suitable for AHPND detection outside a laboratory setting and extremely useful at a pond side location. Isothermal amplification is based on the nucleic acid amplification at a single temperature and does not require the use of a thermal cycler. In this study, we developed an isothermal Recombinase Polymerase Amplification (RPA) assay for AHPND detection targeting both pirA and pirB genes, simultaneously and evaluated the specificity and sensitivity of the assay. The assay could detect AHPND without any cross-reaction with other microbial pathogens and Specific Pathogen Free (SPF) shrimp. The limit of detection of the assay was 5 copies of pirAB genes. To evaluate the reliability of the assay in detecting AHPND, DNA from Penaeus vannamei shrimp displaying acute and chronic infection were analyzed by the RPA assay and the results were compared with SYBR Green real-time PCR assay. While there was a 100% conformity between the two assay while detecting acute phase infection, RPA appeared to be more sensitive in detecting chronic phase infection. The data suggest that RPA assay described here would be a reliable method in detecting AHPND outside a standard laboratory setting.
Collapse
Affiliation(s)
- Hung Nam Mai
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Luis F Aranguren Caro
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Roberto Cruz-Flores
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, 1117 E Lowell St, Tucson, AZ 85721, USA.
| |
Collapse
|
258
|
Zheng C, Wang K, Zheng W, Cheng Y, Li T, Cao B, Jin Q, Cui D. Rapid developments in lateral flow immunoassay for nucleic acid detection. Analyst 2021; 146:1514-1528. [PMID: 33595550 DOI: 10.1039/d0an02150d] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, lateral flow assay (LFA) for nucleic acid detection has drawn increasing attention in the point-of-care testing fields. Due to its rapidity, easy implementation, and low equipment requirement, it is well suited for use in rapid diagnosis, food authentication, and environmental monitoring under source-limited conditions. This review will discuss two main research directions of lateral flow nucleic acid tests. The first one is the incorporation of isothermal amplification methods with LFA, which ensures an ultra-high testing sensitivity under non-laboratory conditions. The two most commonly used methodologies will be discussed, namely Loop-mediated Isothermal Amplification (LAMP) and Recombinase Polymerase Amplification (RPA), and some novel methods with special properties will also be introduced. The second research direction is the development of novel labeling materials. It endeavors to increase the sensitivity and quantifiability of LFA testing, where signals can be read and analyzed by portable devices. These methods are compared in terms of limits of detection, detection times, and quantifiabilities. It is anticipated that future research on lateral flow nucleic acid tests will focus on the integration of the whole testing process into a microfluidic system and the combination with molecular diagnostic tools such as clustered regularly interspaced short palindromic repeats to facilitate a rapid and accurate test.
Collapse
Affiliation(s)
- Chujun Zheng
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai Engineering Research Center for Intelligent diagnosis and treatment instrument, Key Laboratory of Thin Film and Microfabrication Technology (Ministry of Education), Shanghai 200240, China.
| | | | | | | | | | | | | | | |
Collapse
|
259
|
Yukhet P, Buddhachat K, Vilaivan T, Suparpprom C. Isothermal Detection of Canine Blood Parasite ( Ehrlichia canis) Utilizing Recombinase Polymerase Amplification Coupled with Graphene Oxide Quenching-Based Pyrrolidinyl Peptide Nucleic Acid. Bioconjug Chem 2021; 32:523-532. [PMID: 33651604 DOI: 10.1021/acs.bioconjchem.0c00639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Canine monocytic ehrlichiosis (CME), caused by transmitted Ehrlichia canis infection, is a major disease in dogs with worldwide distribution. Herein, a nucleic acid assay was established for the identification of E. canis infection employing a fluorescently labeled conformationally constrained pyrrolidinyl PNA probe (Flu-acpcPNA) designed to sequence-specifically target the 16S rRNA gene. The sensing principle is based on the excellent quenching ability of graphene oxide (GO) of the free PNA probe, that was diminished upon binding to the DNA target. The addition of DNase I improved the performance of the detection system by eliminating the nonspecific quenching capability of long-chain dsDNA and thus enhancing the fluorescence signaling. The assay was coupled with a recombinase polymerase amplification (RPA) technique, which could be performed under isothermal conditions (37 °C) without DNA denaturation and purification steps. The established method is simple to set up and execute, proving a rapid, specific, and sensitive detection of 16S rRNA gene of E. canis with a limit of detection at least 11.1 pM. This technique shows good potential for the visual detection of double-stranded DNA targets without the need for PCR or complicated instruments, which shows great promise for practical usage in resource limited areas.
Collapse
Affiliation(s)
- Phanomsak Yukhet
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand.,Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand
| |
Collapse
|
260
|
Huang P, Jin H, Zhao Y, Li E, Yan F, Chi H, Wang Q, Han Q, Mo R, Song Y, Bi J, Jiao C, Li W, He H, Wang H, Ma A, Feng N, Wang J, Wang T, Yang S, Gao Y, Xia X, Wang H. Nucleic acid visualization assay for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) by targeting the UpE and N gene. PLoS Negl Trop Dis 2021; 15:e0009227. [PMID: 33647020 PMCID: PMC7951983 DOI: 10.1371/journal.pntd.0009227] [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: 09/05/2020] [Revised: 03/11/2021] [Accepted: 02/11/2021] [Indexed: 12/26/2022] Open
Abstract
Since its first emergence in 2012, cases of infection with Middle East respiratory syndrome coronavirus (MERS-CoV) have continued to occur. At the end of January 2020, 2519 laboratory confirmed cases with a case-fatality rate of 34.3% have been reported. Approximately 84% of human cases have been reported in the tropical region of Saudi Arabia. The emergence of MERS-CoV has highlighted need for a rapid and accurate assay to triage patients with a suspected infection in a timely manner because of the lack of an approved vaccine or an effective treatment for MERS-CoV to prevent and control potential outbreaks. In this study, we present two rapid and visual nucleic acid assays that target the MERS-CoV UpE and N genes as a panel that combines reverse transcription recombinase polymerase amplification with a closed vertical flow visualization strip (RT-RPA-VF). This test panel was designed to improve the diagnostic accuracy through dual-target screening after referencing laboratory testing guidance for MERS-CoV. The limit of detection was 1.2×101 copies/μl viral RNA for the UpE assay and 1.2 copies/μl viral RNA for the N assay, with almost consistent with the sensitivity of the RT-qPCR assays. The two assays exhibited no cross-reactivity with multiple CoVs, including the bat severe acute respiratory syndrome related coronavirus (SARSr-CoV), the bat coronavirus HKU4, and the human coronaviruses 229E, OC43, HKU1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, the panel does not require sophisticated equipment and provides rapid detection within 30 min. This panel displays good sensitivity and specificity and may be useful to rapidly detect MERS-CoV early during an outbreak and for disease surveillance.
Collapse
Affiliation(s)
- Pei Huang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hongli Jin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Entao Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hang Chi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Qi Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Qiuxue Han
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruo Mo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Yumeng Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jinhao Bi
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Cuicui Jiao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wujian Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongbin He
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Hongmei Wang
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Aimin Ma
- Changchun Medical College, Changchun, China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jianzhong Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Hualei Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| |
Collapse
|
261
|
Han X, Liu Y, Yin J, Yue M, Mu Y. Microfluidic devices for multiplexed detection of foodborne pathogens. Food Res Int 2021; 143:110246. [PMID: 33992358 DOI: 10.1016/j.foodres.2021.110246] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 01/10/2023]
Abstract
The global burden of foodborne diseases is substantial and foodborne pathogens are the major cause for human illnesses. In order to prevent the spread of foodborne pathogens, detection methods are constantly being updated towards rapid, portable, inexpensive, and multiplexed on-site detection. Due to the nature of the small size and low volume, microfluidics has been applied to rapid, time-saving, sensitive, and portable devices to meet the requirements of on-site detection. Simultaneous detection of multiple pathogens is another key parameter to ensure food safety. Multiplexed detection technology, including microfluidic chip design, offers a new opportunity to achieve this goal. In this review, we introduced several sample preparation and corresponding detection methods on microfluidic devices for multiplexed detection of foodborne pathogens. In the sample preparation section, methods of cell capture and enrichment, as well as nucleic acid sample preparation, were described in detail, and in the section of detection methods, amplification, immunoassay, surface plasmon resonance and impedance spectroscopy were exhaustively illustrated. The limitations and advantages of all available experimental options were also summarized and discussed in order to form a comprehensive understanding of cutting-edge technologies and provide a comparative assessment for future investigation and in-field application.
Collapse
Affiliation(s)
- Xiaoying Han
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310023, PR China; College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yuanhui Liu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310023, PR China; College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310023, PR China
| | - Min Yue
- Department of Veterinary Medicine & Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou 310058, PR China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, PR China; Hainan Institute of Zhejiang University, Sanya 572025, PR China.
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310023, PR China.
| |
Collapse
|
262
|
Ma C, Fan S, Wang Y, Yang H, Qiao Y, Jiang G, Lyu M, Dong J, Shen H, Gao S. Rapid Detection of Enterocytozoon hepatopenaei Infection in Shrimp With a Real-Time Isothermal Recombinase Polymerase Amplification Assay. Front Cell Infect Microbiol 2021; 11:631960. [PMID: 33718281 PMCID: PMC7947341 DOI: 10.3389/fcimb.2021.631960] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Enterocytozoon hepatopenaei (EHP) infection has become a significant threat in shrimp farming industry in recent years, causing major economic losses in Asian countries. As there are a lack of effective therapeutics, prevention of the infection with rapid and reliable pathogen detection methods is fundamental. Molecular detection methods based on polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) have been developed, but improvements on detection speed and convenience are still in demand. The isothermal recombinase polymerase amplification (RPA) assay derived from the recombination-dependent DNA replication (RDR) mechanism of bacteriophage T4 is promising, but the previously developed RPA assay for EHP detection read the signal by gel electrophoresis, which restricted this application to laboratory conditions and hampered the sensitivity. The present study combined fluorescence analysis with the RPA system and developed a real-time RPA assay for the detection of EHP. The detection procedure was completed in 3–7 min at 39°C and showed good specificity. The sensitivity of 13 gene copies per reaction was comparable to the current PCR- and LAMP-based methods, and was much improved than the RPA assay analyzed by gel electrophoresis. For real clinical samples, detection results of the real-time RPA assay were 100% consistent with the industrial standard nested PCR assay. Because of the rapid detection speed and the simple procedure, the real-time RPA assay developed in this study can be easily assembled as an efficient and reliable on-site detection tool to help control EHP infection in shrimp farms.
Collapse
Affiliation(s)
- Chao Ma
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Shihui Fan
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Yu Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Haitao Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Yi Qiao
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Ge Jiang
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Jingquan Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| |
Collapse
|
263
|
Mustafa MI, Makhawi AM. SHERLOCK and DETECTR: CRISPR-Cas Systems as Potential Rapid Diagnostic Tools for Emerging Infectious Diseases. J Clin Microbiol 2021; 59:e00745-20. [PMID: 33148705 PMCID: PMC8106734 DOI: 10.1128/jcm.00745-20] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Infectious diseases are one of the most intimidating threats to human race, responsible for an immense burden of disabilities and deaths. Rapid diagnosis and treatment of infectious diseases offers a better understanding of their pathogenesis. According to the World Health Organization, the ideal approach for detecting foreign pathogens should be rapid, specific, sensitive, instrument-free, and cost-effective. Nucleic acid pathogen detection methods, typically PCR, have numerous limitations, such as highly sophisticated equipment requirements, reagents, and trained personnel relying on well-established laboratories, besides being time-consuming. Thus, there is a crucial need to develop novel nucleic acid detection tools that are rapid, specific, sensitive, and cost-effective, particularly ones that can be used for versatile point-of-care diagnostic applications. Two new methods exploit unpredicted in vitro properties of CRISPR-Cas effectors, turning activated nucleases into basic amplifiers of a specific nucleic acid binding event. These effectors can be attached to a diversity of reporters and utilized in tandem with isothermal amplification approaches to create sensitive identification in multiple deployable field formats. Although still in their beginning, SHERLOCK and DETECTR technologies are potential methods for rapid detection and identification of infectious diseases, with ultrasensitive tests that do not require complicated processing. This review describes SHERLOCK and DETECTR technologies and assesses their properties, functions, and prospective to become the ultimate diagnostic tools for diagnosing infectious diseases and curbing disease outbreaks.
Collapse
|
264
|
Ichzan AM, Hwang SH, Cho H, Fang CS, Park S, Kim G, Kim J, Nandhakumar P, Yu B, Jon S, Kim KS, Yang H. Solid-phase recombinase polymerase amplification using an extremely low concentration of a solution primer for sensitive electrochemical detection of hepatitis B viral DNA. Biosens Bioelectron 2021; 179:113065. [PMID: 33578116 DOI: 10.1016/j.bios.2021.113065] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/15/2022]
Abstract
Recombinase polymerase amplification (RPA) is considered one of the best amplification methods for realizing a miniaturized diagnostic instrument; however, it is notably challenging to obtain low detection limits in solid-phase RPA. To overcome these difficulties, we combined solid-phase RPA with electrochemical detection and used a new concentration combination of three primers (surface-bound forward primer, solution reverse primer, and an extremely low concentration of solution forward primer). When solid-phase RPA was performed on an indium tin oxide (ITO) electrode modified with a surface-bound forward primer in a solution containing a biotin-terminated solution reverse primer, an extremely low concentration of a solution forward primer, and a template DNA or genomic DNA for a target gene of hepatitis B virus (HBV), amplification occurred mainly in solution until all the solution forward primers were consumed. Subsequently, DNA amplicons produced in solution participated in solid-phase amplification involving surface-bound forward primer and solution reverse primer. Afterward, neutravidin-conjugated DT-diaphorase (DT-D) was attached to a biotin-terminated DNA amplicon on the ITO electrode. Finally, chronocoulometric charges were measured using electrochemical-enzymatic redox cycling involving the ITO electrode, 1,4-naphthoquinone, DT-D, and reduced β-nicotinamide adenine dinucleotide. The detection limit for HBV was measured using microfabricated electrodes and was found to be approximately 0.1 fM. This proposed method demonstrated better amplification efficiency for HBV genomic DNA than solid-phase RPA without using additional solution primer and asymmetric solid-phase RPA.
Collapse
Affiliation(s)
- Andi Muhammad Ichzan
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan, College of Medicine, Seoul, 05505, Republic of Korea
| | - Hyejin Cho
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Chiew San Fang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Seonhwa Park
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Gyeongho Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Jihyeon Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Ponnusamy Nandhakumar
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Byeongjun Yu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sangyong Jon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Kwang-Sun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea.
| | - Haesik Yang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea.
| |
Collapse
|
265
|
Rani A, Ravindran VB, Surapaneni A, Shahsavari E, Haleyur N, Mantri N, Ball AS. Evaluation and comparison of recombinase polymerase amplification coupled with lateral-flow bioassay for Escherichia coli O157:H7 detection using diifeerent genes. Sci Rep 2021; 11:1881. [PMID: 33479307 PMCID: PMC7820579 DOI: 10.1038/s41598-021-81312-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022] Open
Abstract
Shiga toxin-producing Escherichia coli serotype O157:H7 is a food and waterborne zoonotic pathogen causing gastroenteritis in humans. Rapid and simple detection in water and food is imperative to control its spread. However, traditional microbial detection approaches are time-consuming, expensive and complex to operate at the point-of-care without professional training. We present a rapid, simple, sensitive, specific and portable method for detection of E. coli O157:H7 in drinking water, apple juice and milk. We evaluated the effect of gene selection in detecting E. coli O157:H7 using recombinase polymerase amplification coupled with a lateral flow assay using rfbE, fliC and stx gene targets. As low as 100 ag and 1 fg DNA, 4-5 CFU/mL and 101 CFU/mL of E. coli O157:H7 was detected using the stx and rfbE gene targets respectively with 100% specificity, whilst the detection limit was 10 fg DNA and 102 CFU/mL for the fliC gene target, with 72.8% specificity. The RPA-LFA can be completed within 8 min at temperatures between 37 and 42 °C with reduced handling and simple equipment requirements. The test threshold amplification of the target was achieved in 5-30 min of incubation. In conclusion, RPA-LFA represents a potential rapid and effective alternative to conventional methods for the monitoring of E. coli O157:H7 in food and water.
Collapse
Affiliation(s)
- Alka Rani
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia.
| | - Vivek B Ravindran
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia
| | - Aravind Surapaneni
- South East Water, Frankston, VIC, Australia.,ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora West, VIC, 3083, Australia
| | | | | | - Nitin Mantri
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, 3083, Australia
| | - Andrew S Ball
- School of Science, RMIT University, Bundoora West, VIC, 3083, Australia.,ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Bundoora West, VIC, 3083, Australia
| |
Collapse
|
266
|
Huergo MAC, Thanh NTK. Current advances in the detection of COVID-19 and evaluation of the humoral response. Analyst 2021; 146:382-402. [PMID: 33410826 DOI: 10.1039/d0an01686a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The new outbreak caused by coronavirus SARS-CoV-2 started at the end of 2019 and was declared a pandemic in March 2020. Since then, several diagnostic approaches have been re-adapted, and also improved from the previous detections of SARS and MERS coronavirus. The best strategy to handle this situation seems to rely on a triad of detection methods: (i) highly sensitive and specific techniques as the gold standard method, (ii) easier and faster point of care tests accessible for large population screening, and (iii) serology assays to complement the direct detection and to use for surveillance. In this study, we assessed the techniques and tests described in the literature, their advantages and disadvantages, and the interpretation of the results. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is undoubtedly the gold standard technique utilized not only for diagnostics, but also as a standard for comparison and validation of newer approaches. Other nucleic acid amplification methods have been shown to be adequate as point of care (POC) diagnostic tests with similar performance as RT-qPCR. The analysis of seroconversion with immunotests shows the complexity of the immune response to COVID-19. The detection of anti-SARS-CoV-2 antibodies can also help to detect previously infected asymptomatic individuals with negative RT-qPCR tests. Nevertheless, more controlled serology cohort studies should be performed as soon as possible to understand the immune response to SARS-CoV-2.
Collapse
Affiliation(s)
- Maria Ana Cristina Huergo
- Theoretical and Applied Physical Chemical Research Institute (INIFTA), National Univesity of La Plata (UNLP), CONICET. Sucursal 4 Casilla de Correo 16, 1900 La Plata, Argentina.
| | | |
Collapse
|
267
|
McQuillan JS, Wilson MW. Recombinase polymerase amplification for fast, selective, DNA-based detection of faecal indicator Escherichia coli. Lett Appl Microbiol 2021; 72:382-389. [PMID: 33175415 DOI: 10.1111/lam.13427] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/01/2022]
Abstract
The bacterium Escherichia coli is commonly associated with the presence of faecal contamination in environmental samples, and is therefore subject to statutory surveillance. This is normally done using a culture-based methodology, which can be slow and laborious. Nucleic acid amplification for the detection of E. coli DNA sequences is a significantly more rapid approach, suited for applications in the field such as a point of sample analysis, and to provide an early warning of contamination. An existing, high integrity qPCR method to detect the E. coli ybbW gene, which requires almost an hour to detect low quantities of the target, was compared with a novel, isothermal RPA method, targeting the same sequence but achieving the result within a few minutes. The RPA technique demonstrated equivalent inclusivity and selectivity, and was able to detect DNA extracted from 100% of 99 E. coli strains, and exclude 100% of 30 non-target bacterial species. The limit of detection of the RPA assay was at least 100 target sequence copies. The high speed and simple, isothermal amplification chemistry may indicate that RPA is a more suitable methodology for on-site E. coli monitoring than an existing qPCR technique.
Collapse
Affiliation(s)
- J S McQuillan
- National Oceanography Centre, Southampton, SO14 3ZH, UK
| | - M W Wilson
- National Oceanography Centre, Southampton, SO14 3ZH, UK
| |
Collapse
|
268
|
Rezaei M, Razavi Bazaz S, Zhand S, Sayyadi N, Jin D, Stewart MP, Ebrahimi Warkiani M. Point of Care Diagnostics in the Age of COVID-19. Diagnostics (Basel) 2020; 11:E9. [PMID: 33374612 PMCID: PMC7822494 DOI: 10.3390/diagnostics11010009] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022] Open
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated serious respiratory disease, coronavirus disease 2019 (COVID-19), poses a major threat to global public health. Owing to the lack of vaccine and effective treatments, many countries have been overwhelmed with an exponential spread of the virus and surge in the number of confirmed COVID-19 cases. Current standard diagnostic methods are inadequate for widespread testing as they suffer from prolonged turn-around times (>12 h) and mostly rely on high-biosafety-level laboratories and well-trained technicians. Point-of-care (POC) tests have the potential to vastly improve healthcare in several ways, ranging from enabling earlier detection and easier monitoring of disease to reaching remote populations. In recent years, the field of POC diagnostics has improved markedly with the advent of micro- and nanotechnologies. Due to the COVID-19 pandemic, POC technologies have been rapidly innovated to address key limitations faced in existing standard diagnostic methods. This review summarizes and compares the latest available POC immunoassay, nucleic acid-based and clustered regularly interspaced short palindromic repeats- (CRISPR)-mediated tests for SARS-CoV-2 detection that we anticipate aiding healthcare facilities to control virus infection and prevent subsequent spread.
Collapse
Affiliation(s)
- Meysam Rezaei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
| | - Sareh Zhand
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
| | - Nima Sayyadi
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University Sydney, Sydney, NSW 2109, Australia
| | - Dayong Jin
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
| | - Martin P. Stewart
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia; (M.R.); (S.R.B.); (S.Z.); (N.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW 2007, Australia; (D.J.); (M.P.S.)
- SUStech-UTS Joint Research Centre for Biomedical Materials & Devices, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Molecular Medicine, Sechenov University, 119991 Moscow, Russia
| |
Collapse
|
269
|
Subsoontorn P, Lohitnavy M, Kongkaew C. The diagnostic accuracy of isothermal nucleic acid point-of-care tests for human coronaviruses: A systematic review and meta-analysis. Sci Rep 2020; 10:22349. [PMID: 33339871 PMCID: PMC7749114 DOI: 10.1038/s41598-020-79237-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/04/2020] [Indexed: 02/01/2023] Open
Abstract
Many recent studies reported coronavirus point-of-care tests (POCTs) based on isothermal amplification. However, the performances of these tests have not been systematically evaluated. Cochrane Handbook for Systematic Reviews of Diagnostic Test Accuracy was used as a guideline for conducting this systematic review. We searched peer-reviewed and preprint articles in PubMed, BioRxiv and MedRxiv up to 28 September 2020 to identify studies that provide data to calculate sensitivity, specificity and diagnostic odds ratio (DOR). Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) was applied for assessing quality of included studies and Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies (PRISMA-DTA) was followed for reporting. We included 81 studies from 65 research articles on POCTs of SARS, MERS and COVID-19. Most studies had high risk of patient selection and index test bias but low risk in other domains. Diagnostic specificities were high (> 0.95) for included studies while sensitivities varied depending on type of assays and sample used. Most studies (n = 51) used reverse transcription loop-mediated isothermal amplification (RT-LAMP) to diagnose coronaviruses. RT-LAMP of RNA purified from COVID-19 patient samples had pooled sensitivity at 0.94 (95% CI: 0.90-0.96). RT-LAMP of crude samples had substantially lower sensitivity at 0.78 (95% CI: 0.65-0.87). Abbott ID Now performance was similar to RT-LAMP of crude samples. Diagnostic performances by CRISPR and RT-LAMP on purified RNA were similar. Other diagnostic platforms including RT- recombinase assisted amplification (RT-RAA) and SAMBA-II also offered high sensitivity (> 0.95). Future studies should focus on the use of un-bias patient cohorts, double-blinded index test and detection assays that do not require RNA extraction.
Collapse
Affiliation(s)
- Pakpoom Subsoontorn
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
| | - Manupat Lohitnavy
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, Thailand
- Center of Excellence for Environmental Health and Toxicology, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Chuenjid Kongkaew
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, Thailand
- Research Centre for Safety and Quality in Health, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, 65000, Thailand
- Research Department of Practice and Policy, UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK
| |
Collapse
|
270
|
Rungkamoltip P, Temisak S, Piboonprai K, Japrung D, Thangsunan P, Chanpanitkitchot S, Chaowawanit W, Chandeying N, Tangjitgamol S, Iempridee T. Rapid and ultrasensitive detection of circulating human papillomavirus E7 cell-free DNA as a cervical cancer biomarker. Exp Biol Med (Maywood) 2020; 246:654-666. [PMID: 33307803 DOI: 10.1177/1535370220978899] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has attracted attention as a non-invasive biomarker for diagnosing and monitoring various cancers. Given that human papillomavirus (HPV) DNA integration and overexpression of E6/E7 oncogenes are pivotal events for carcinogenesis, we sought to determine if HPV E7 cfDNA could serve as a specific biomarker for cervical cancer detection. We applied droplet digital PCR (ddPCR) to quantify HPV16/18 E7 cfDNA from the serum of patients with cervical cancer, cervical intraepithelial neoplasia, and controls. HPV16/18 E7 cfDNA was highly specific for cervical cancer, displaying 30.77% sensitivity, 100% specificity, and an area under the curve of 0.65. Furthermore, we developed a sensitive isothermal detection of HPV16/18 E7 and the PIK3CA WT reference gene based on recombinase polymerase amplification combined with a lateral flow strip (RPA-LF). The assay took less than 30 min and the detection limit was 5-10 copies. RPA-LF exhibited 100% sensitivity and 88.24% specificity towards HPV16/18 E7 cfDNA in clinical samples. The agreement between RPA-LF and ddPCR was 83.33% (κ = 0.67) for HPV16 E7 and 100% (κ = 1.0) for HPV18 E7, indicating a good correlation between both tests. Therefore, we conclude that HPV E7 cfDNA represents a potential tumor marker with excellent specificity and moderate sensitivity for minimally invasive cervical cancer monitoring. Moreover, the RPA-LF assay provides an affordable, rapid, and ultrasensitive tool for detecting HPV cfDNA in resource-limited settings.
Collapse
Affiliation(s)
- Phetploy Rungkamoltip
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Sasithon Temisak
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Kitiya Piboonprai
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand.,Laboratory of Host Defense, The World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pattanapong Thangsunan
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Saranya Chanpanitkitchot
- Department of Obstetrics and Gynecology, Rajavithi Hospital, College of Medicine, Rangsit University, Bangkok 10400, Thailand
| | - Woraphot Chaowawanit
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Nutthaporn Chandeying
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Siriwan Tangjitgamol
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand.,Obstetrics and Gynecology Section, MedPark Hospital, Bangkok 10110, Thailand
| | - Tawin Iempridee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| |
Collapse
|
271
|
Wang L, He K, Sadak O, Wang X, Wang Q, Xu X. Visual detection of in vitro nucleic acid replication by submicro- and nano-sized materials. Biosens Bioelectron 2020; 169:112602. [PMID: 32947078 DOI: 10.1016/j.bios.2020.112602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/29/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022]
Abstract
The rapid growth of in vitro nucleic acid replication has offered a powerful tool for clinical diagnosis, food safety detection and environmental monitorning. Successful implementation of various isothermal nucleic acid amplification methods enables rapid replication of target sequences without the participant of a thermal cycler. Point-of-need analysis possesses great superiorities in user-friendly, instant results analysis, low manufacturing, and consumable costs. To meet the great challenge of point-of-need analysis, developing simple and rapid visual methods becomes crucial. Submicro- and nanomaterials possess unique surface properties, which enables their rapid response to DNA amplicons. Their unique optical, magnetic, catalytic, and other physical/chemical properties have been frequently employed for the visual detection of in vitro nucleic acid replications. Herein, we aim to review the submicro- and nanomaterials-based visual methods for detection of nucleic acid amplification. The visual methods are classified according to the designing strategies (e.g. LSPR, bridging flocculation, luminescence, catalytic reaction, separation, etc.). The basic principles, merits and drawbacks of each strategy are described. The application in analysis of nucleic acid targets and non-nucleic acid targets are discussed. The main challenges and future research directions are also highlighted in this rapidly emerging field.
Collapse
Affiliation(s)
- Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Omer Sadak
- Department of Electrical and Electronics Engineering, Ardahan University, 75000, Turkey
| | - Xinquan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Qiang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| |
Collapse
|
272
|
Xu X, Luo T, Gao J, Lin N, Li W, Xia X, Wang J. CRISPR-Assisted DNA Detection: A Novel dCas9-Based DNA Detection Technique. CRISPR J 2020; 3:487-502. [PMID: 33346711 DOI: 10.1089/crispr.2020.0041] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nucleic acid detection techniques are always critical to diagnosis, especially in the background of the present coronavirus disease 2019 pandemic. Simple and rapid detection techniques with high sensitivity and specificity are always urgently needed. However, current nucleic acid detection techniques are still limited by traditional amplification and hybridization. To overcome this limitation, here we developed CRISPR-Cas9-assisted DNA detection (CADD). In this detection, a DNA sample is incubated with a pair of capture single guide RNAs (sgRNAs; sgRNAa and sgRNAb) specific to a target DNA, dCas9, a signal readout-related probe, and an oligo-coated solid support beads or microplate at room temperature (RT) for 15 min. During this incubation, the dCas9-sgRNA-DNA complex is formed and captured on solid support by the capture sequence of sgRNAa, and the signal readout-related probe is captured by the capture sequence of sgRNAb. Finally, the detection result is reported by a fluorescent or colorimetric signal readout. This detection was verified by detecting DNA of bacteria, cancer cells, and viruses. In particular, by designing a set of sgRNAs specific to 15 high-risk human papillomaviruses (HPVs), the HPV infection in 64 clinical cervical samples was successfully detected by the method. All detections can be finished in 30 min at RT. This detection holds promise for rapid on-the-spot detection or point-of-care testing.
Collapse
Affiliation(s)
- Xinhui Xu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China
| | - Tao Luo
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China
| | - Jinliang Gao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China
| | - Na Lin
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China
| | - Weiwei Li
- Jinling Hospital, Nanjing University School of Medicine, Nanjing, PR China
| | - Xinyi Xia
- Jinling Hospital, Nanjing University School of Medicine, Nanjing, PR China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, PR China
| |
Collapse
|
273
|
Pang Y, Cong F, Zhang X, Li H, Chang YF, Xie Q, Lin W. A recombinase polymerase amplification-based assay for rapid detection of Chlamydia psittaci. Poult Sci 2020; 100:585-591. [PMID: 33518111 PMCID: PMC7858173 DOI: 10.1016/j.psj.2020.11.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/06/2020] [Accepted: 11/22/2020] [Indexed: 11/22/2022] Open
Abstract
Chlamydia psittaci is a zoonotic agent of systemic wasting disease in birds and atypical pneumonia in mammalians including humans, constituting a public health risk. A rapid diagnostic assay would be beneficial in screening C. psittaci in the field. In this study, we developed a probe-based recombinase polymerase amplification (RPA) assay for the rapid detection of C. psittaci. The specific primer pairs and probe targeting the conserved region of the outer membrane protein A gene were designed and applied to the real-time real-time RPA assay. The test can be performed at 39°C for 20 min using a portable device, with sensitivities approaching 100 copies of DNA molecules per reaction, with no cross-reaction with other pathogens. The clinical performance of the RPA assay was evaluated in an outbreak of C. psittaci and has high accuracy levels in field applications. The epidemic C. psittaci strains were classed into 2 genotypes: A and C. Collectively, this study offers a promising approach in screening for C. psittaci both in a laboratory setting and in field settings, and RPA can be used as an effective clinical test to monitor outbreaks in domestic fowl populations.
Collapse
Affiliation(s)
- Yanling Pang
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Feng Cong
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510633, P.R. China
| | - Xinheng Zhang
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Hongxin Li
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Qingmei Xie
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Wencheng Lin
- Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou 510642, P.R. China; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
274
|
Khan P, Aufdembrink LM, Engelhart AE. Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings. ACS Synth Biol 2020; 9:2861-2880. [PMID: 32966744 PMCID: PMC7552996 DOI: 10.1021/acssynbio.0c00359] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Indexed: 02/06/2023]
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, poses grave threats to both the global economy and health. The predominant diagnostic screens in use for SARS-CoV-2 detection are molecular techniques such as nucleic acid amplification tests. In this Review, we compare current and emerging isothermal diagnostic methods for COVID-19. We outline the molecular and serological techniques currently being used to detect SARS-CoV-2 infection, past or present, in patients. We also discuss ongoing research on isothermal techniques, CRISPR-mediated detection assays, and point-of-care diagnostics that have potential for use in SARS-CoV-2 detection. Large-scale viral testing during a global pandemic presents unique challenges, chief among them the simultaneous need for testing supplies, durable equipment, and personnel in many regions worldwide, with each of these regions possessing testing needs that vary as the pandemic progresses. The low-cost isothermal technologies described in this Review provide a promising means by which to address these needs and meet the global need for testing of symptomatic individuals as well as provide a possible means for routine testing of asymptomatic individuals, providing a potential means of safely enabling reopenings and early monitoring of outbreaks.
Collapse
Affiliation(s)
- Pavana Khan
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
| | - Lauren M. Aufdembrink
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
| | - Aaron E. Engelhart
- Department of Genetics, Cell Biology, and Development,
University of Minnesota, 6-160 Jackson Hall, 321 Church
Street SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
275
|
Cheng Q, Parvin B. Rapid identification of a subset of foodborne bacteria in live-cell assays. Appl Microbiol Biotechnol 2020; 104:10571-10584. [PMID: 33185701 DOI: 10.1007/s00253-020-10970-9] [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: 02/20/2020] [Revised: 09/06/2020] [Accepted: 10/21/2020] [Indexed: 11/28/2022]
Abstract
The detection and identification of microbial pathogens in meat and fresh produce play an essential role in food safety for reducing foodborne illnesses every year. A new approach based on targeting a specific sequence of the 16S rRNA region for each bacterium is proposed and validated. The probe complex consists of a C60, a conjugated RNA detector which targets a specific 16S rRNA sequence, and a complementary fluorescent reporter. The RNA detectors were designed by integrating NIH nucleotide and Vienna RNA Webservice databases, and their specificities were validated by the RDP database. Probe complexes were synthesized for identifying E. coli K12, E. coli O157: H7, S. enterica, Y. enterocolitica, C. perfringens, and L. monocytogenes. First, under controlled conditions of known bacterial mixtures, the efficiency and crosstalk for identifying the foodborne bacteria were quantified to be above 94% and below 5%, respectively. Second, experiments were designed by inoculating meat products by known numbers of bacteria and measuring the limit of detection. In one experiment, 225 g of autoclaved ground chicken was inoculated with 9 E. coli O157:H7, where 6.8 ± 1.2 bacteria with 95% confidence interval were recovered. Third, by positionally printing probe complexes in microwells, specific microorganisms were identified with only one fluorophore. The proposed protocol is a cell-based system, can identify live bacteria in 15 min, requires no amplification, and has the potential to open new surveillance opportunities.Key points• The identification of foodborne bacteria is enabled in live-cell assays.• The limit of detection for 100 g of fresh chicken breast inoculated with 4 bacteria is 2.7 ± 1.4 with 95% confidence interval.• The identification of five bacteria in a coded microwell chip is enabled with only one fluorophore.
Collapse
Affiliation(s)
- Qingsu Cheng
- Department of Electrical and Biomedical Engineering, University of Nevada, Reno, 1664 N. Virginia St., NV, 89557, Reno, USA.,Department of Cell and Molecular Biology, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA
| | - Bahram Parvin
- Department of Electrical and Biomedical Engineering, University of Nevada, Reno, 1664 N. Virginia St., NV, 89557, Reno, USA. .,Department of Cell and Molecular Biology, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA.
| |
Collapse
|
276
|
Bhunia AK, Bisha B, Gehring AG, Brehm-Stecher BF. Advances in Foodborne Pathogen Analysis. Foods 2020; 9:foods9111635. [PMID: 33182540 PMCID: PMC7696508 DOI: 10.3390/foods9111635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022] Open
Abstract
As the world population has grown, new demands on the production of foods have been met by increased efficiencies in production, from planting and harvesting to processing, packaging and distribution to retail locations. These efficiencies enable rapid intranational and global dissemination of foods, providing longer “face time” for products on retail shelves and allowing consumers to make healthy dietary choices year-round. However, our food production capabilities have outpaced the capacity of traditional detection methods to ensure our foods are safe. Traditional methods for culture-based detection and characterization of microorganisms are time-, labor- and, in some instances, space- and infrastructure-intensive, and are therefore not compatible with current (or future) production and processing realities. New and versatile detection methods requiring fewer overall resources (time, labor, space, equipment, cost, etc.) are needed to transform the throughput and safety dimensions of the food industry. Access to new, user-friendly, and point-of-care testing technologies may help expand the use and ease of testing, allowing stakeholders to leverage the data obtained to reduce their operating risk and health risks to the public. The papers in this Special Issue on “Advances in Foodborne Pathogen Analysis” address critical issues in rapid pathogen analysis, including preanalytical sample preparation, portable and field-capable test methods, the prevalence of antibiotic resistance in zoonotic pathogens and non-bacterial pathogens, such as viruses and protozoa.
Collapse
Affiliation(s)
- Arun K. Bhunia
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Comparative Pathobiology (Courtesy), Purdue University, West Lafayette, IN 47907, USA
- Correspondence: (A.K.B.); (B.B.); (A.G.G.); (B.F.B.-S.); Tel.: +1-765-494-5443 (A.K.B.); +1-307-766-3140 (B.B.); +1-215-233-6491 (A.G.G.); +1-515-294-6469 (B.F.B.-S.)
| | - Bledar Bisha
- Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA
- Correspondence: (A.K.B.); (B.B.); (A.G.G.); (B.F.B.-S.); Tel.: +1-765-494-5443 (A.K.B.); +1-307-766-3140 (B.B.); +1-215-233-6491 (A.G.G.); +1-515-294-6469 (B.F.B.-S.)
| | - Andrew G. Gehring
- Molecular Characterization of Foodborne Pathogens, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
- Correspondence: (A.K.B.); (B.B.); (A.G.G.); (B.F.B.-S.); Tel.: +1-765-494-5443 (A.K.B.); +1-307-766-3140 (B.B.); +1-215-233-6491 (A.G.G.); +1-515-294-6469 (B.F.B.-S.)
| | - Byron F. Brehm-Stecher
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA
- Correspondence: (A.K.B.); (B.B.); (A.G.G.); (B.F.B.-S.); Tel.: +1-765-494-5443 (A.K.B.); +1-307-766-3140 (B.B.); +1-215-233-6491 (A.G.G.); +1-515-294-6469 (B.F.B.-S.)
| |
Collapse
|
277
|
Kojima K, Juma KM, Akagi S, Hayashi K, Takita T, O'Sullivan CK, Fujiwara S, Nakura Y, Yanagihara I, Yasukawa K. Solvent engineering studies on recombinase polymerase amplification. J Biosci Bioeng 2020; 131:219-224. [PMID: 33177003 DOI: 10.1016/j.jbiosc.2020.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 11/24/2022]
Abstract
Recombinase polymerase amplification (RPA) is a technique that is used to specifically amplify a target nucleic acid sequence. Unlike the polymerase chain reaction (PCR), RPA is performed at a constant temperature between 37 and 42°C. Therefore, it can be potentially used for the onsite detection of various pathogens when combined with DNA extraction and amplicon detection techniques. In this study, we prepared recombinant recombinase and single-stranded DNA-binding protein from T4 phage and used them to examine the effects of reaction conditions and additives on the efficiency of RPA. The results revealed that the optimal pH was 7.5-8.0, optimal potassium acetate concentration was 40-80 mM, and optimal reaction temperature was 37-45°C although dimethyl sulfoxide at 5% v/v and formamide at 5% v/v inhibited the reaction. Our results suggest that RPA could be conducted using a wider range of optimal reaction conditions than those required for PCR and that RPA is highly suitable for point-of-care use.
Collapse
Affiliation(s)
- Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Shihomi Akagi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kaichi Hayashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, Hyogo 669-1337, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka 594-1101, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka 594-1101, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| |
Collapse
|
278
|
Xu Y, Wu P, Zhang H, Li J. Rapid detection of Mycobacterium tuberculosis based on antigen 85B via real-time recombinase polymerase amplification. Lett Appl Microbiol 2020; 72:106-112. [PMID: 32726877 DOI: 10.1111/lam.13364] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 11/29/2022]
Abstract
Tuberculosis (TB), as a common infectious disease, still remains a severe challenge to public health. Due to the unsatisfied clinical needs of currently available diagnostic vehicles, it is desired to establish a new approach for universally detecting Mycobacterium tuberculosis. Herein, we designed a real-time recombinase polymerase amplification (RPA) technology for identifying M. tuberculosis within 20 min at 39°C via custom-designed oligonucleotide primers and probe, which could specifically target antigen 85B (Ag85B). Particularly, the primers F4-R4 produced the fastest fluorescence signal with the probe among four pairs of designed primers in the RPA assays. The optimal primers/probe combination could effectively identify M. tuberculosis with the detection limit of 4·0 copies per μl, as it could not show a positive signal for the genomic DNA from other mycobacteria or pathogens. The Ag85B-based RPA could determine the genomic DNA extracted from M. tuberculosis with high reliability (100%, 22/22). More importantly, when testing clinical sputum samples, the real-time RPA displayed an admirable sensitivity (90%, 95% CI: 80·0-96·0%) and specificity (98%, 95% CI: 89·0-100·0%) compared to traditional smear microscopy, which was similar to the assay of Xpert MTB/RIF. This real-time RPA based Ag85B provides a promising strategy for the rapid and universal diagnosis of TB.
Collapse
Affiliation(s)
- Y Xu
- Department of Infectious Diseases, the First Affiliated Hospital of Nanjing Medical University, Nanjing, PR China.,Department of Infectious Diseases, the Affiliated Zhongda Hospital of Southeast University, Nanjing, PR China
| | - P Wu
- Department of Infectious Diseases, the Affiliated Zhongda Hospital of Southeast University, Nanjing, PR China
| | - H Zhang
- Department of Microbial Inspection, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, PR China
| | - J Li
- Department of Infectious Diseases, the First Affiliated Hospital of Nanjing Medical University, Nanjing, PR China
| |
Collapse
|
279
|
Yang X, Zhang X, Wang Y, Shen H, Jiang G, Dong J, Zhao P, Gao S. A Real-Time Recombinase Polymerase Amplification Method for Rapid Detection of Vibrio vulnificus in Seafood. Front Microbiol 2020; 11:586981. [PMID: 33240242 PMCID: PMC7677453 DOI: 10.3389/fmicb.2020.586981] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
As an important foodborne pathogen, Vibrio vulnificus gives a significant threat to food safety and public health. Rapid and accurate detection methods for V. vulnificus are required to control its spread. The conventional detection methods are time-consuming and labor-intensive, while the polymerase chain reaction (PCR)- and quantitative PCR (qPCR)-based methods are limited because of their dependence on laboratory equipment. Nucleic acid isothermal amplification technologies have been applied to develop simpler assays. In this study, a rapid detection method based on real-time recombinase polymerase amplification (RPA) targeting the extracellular metalloprotease (empV) gene of V. vulnificus has been established. The method finished the detection in 2–14 min at 39°C with good specificity. The limit of detection was 17 gene copies or 1 colony-forming unit (CFU) per reaction, or 1 CFU/10 g of spiked food with enrichment. In a clinical sample detection test, the results of real-time RPA were 100% consistent with bioassay and qPCR. Moreover, the method could resist the effect of food matrix and could tolerate crude templates. The real-time RPA method established in this study is rapid and simple and has the potential to be widely applied for V. vulnificus detection in food safety control.
Collapse
Affiliation(s)
- Xiaohan Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Xue Zhang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Yu Wang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Ge Jiang
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, China
| | - Jingquan Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Panpan Zhao
- Key Laboratory of Zoonosis Research by Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| |
Collapse
|
280
|
Behrmann O, Bachmann I, Hufert F, Dame G. Schnellnachweis von SARS-CoV-2 mit recombinase polymerase amplification. BIOSPEKTRUM 2020; 26:624-627. [PMID: 33078045 PMCID: PMC7556600 DOI: 10.1007/s12268-020-1458-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractThe COVID-19 pandemic highlights the need for fast and simple assays for nucleic acid detection. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. RPA uses recombination proteins in combination with a DNA polymerase for rapid amplification of target DNA at a constant temperature (39–42 °C) within 10 to 20 minutes and can be monitored in real-time with fluorescent probes.
Collapse
Affiliation(s)
- Ole Behrmann
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
- Professur für Sensoren, Institut für Mikrosystemtechnik (IMTEK), Universität, Freiburg, Deutschland
| | - Iris Bachmann
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
| | - Frank Hufert
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
| | - Gregory Dame
- Institut für Mikrobiologie und Virologie, Medizinische Hochschule Brandenburg Theodor Fontane (MHB), Universitätsplatz 1, D-01968 Senftenberg, Deutschland
| |
Collapse
|
281
|
El-Tholoth M, Mauk MG, Elnaker YF, Mosad SM, Tahoun A, El-Sherif MW, Lokman MS, Kassab RB, Abdelsadik A, Saleh AA, Elmahallawy EK. Molecular Characterization and Developing a Point-of-Need Molecular Test for Diagnosis of Bovine Papillomavirus (BPV) Type 1 in Cattle from Egypt. Animals (Basel) 2020; 10:E1929. [PMID: 33096600 PMCID: PMC7588879 DOI: 10.3390/ani10101929] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 12/11/2022] Open
Abstract
Bovine papillomatosis is a viral disease of cattle causing cutaneous warts. A diagnosis of this viral infection is very mandatory for combating the resulting economic losses. Given the limited data available about bovine papillomavirus (BPV) in Egypt, the present study involved the molecular diagnosis of bovine papillomavirus type-1 (BPV-1), -2, -4, -5, and -10 in cattle presenting cutaneous warts on the head and neck from New Valley Province, Egypt. The phylogenetic analysis of the detected types of BPV was also performed, followed by developing a point-of-need molecular assay for the rapid identification of identified BPV types. In this regard, a total of 308 cattle from private farms in Egypt were clinically examined, of which 13 animals presented cutaneous warts due to suspected BPV infection. The symptomatic animals were treated surgically, and biopsies from skin lesions were collected for BPV-1, -2, -4, -5, and -10 molecular identification using polymerase chain reaction (PCR). The presence of BPV-1 DNA was confirmed in 11 collected samples (84.6%), while BPV-2, -4, -5, and -10 were not detected. Sequencing of the PCR products suggested the Egyptian virus is closely related to BPV found in India. An isothermal nucleic acid amplification test (NAAT) with labeled primers specific for the BPV-1 L1 gene sequence, and based on recombinase polymerase amplification (RPA), in combination with a lateral flow strip assay for the detection of RPA products, was developed and tested. The point-of-need molecular assay demonstrated a diagnostic utility comparable to PCR-based testing. Taken together, the present study provides interesting molecular data related to the occurrence of BPV-1 in Egypt and reveals the genetic relatedness of the Egyptian BPV-1 with BPV-1 found in buffalo in India. In addition, a simple, low-cost combined test was also validated for diagnosis of the infection. The present study suggests the necessity of future investigations about the circulating strains of the virus among the cattle in Egypt to assess their genetic relatedness and better understand the epidemiological pattern of the disease.
Collapse
Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; (M.E.-T.); (S.M.M.)
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Health Sciences Division, Veterinary Sciences Program, Al Ain Men’s Campus, Higher Colleges of Technology, Al Ain 17155, UAE
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Yasser F. Elnaker
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, The New Valley University, El-Karga 72511, New Valley, Egypt;
| | - Samah M. Mosad
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; (M.E.-T.); (S.M.M.)
| | - Amin Tahoun
- Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelshkh University, Kafrelsheikh 33511, Egypt;
| | - Mohamed W. El-Sherif
- Department of Surgery, Anesthesiology and Radiology, Faculty of Veterinary Medicine, The New Valley University, El-Karga 72511, New Valley, Egypt;
| | - Maha S. Lokman
- Biology Department, College of Science and Humanities, Prince Sattam bin Abdul Aziz University, Alkharj 11942, Saudi Arabia;
- Department of Zoology and Entomology, Faculty of Science, Helwan University, 11795 Cairo, Egypt;
| | - Rami B. Kassab
- Department of Zoology and Entomology, Faculty of Science, Helwan University, 11795 Cairo, Egypt;
- Department of Biology, Faculty of Science and Arts, Al Baha University, Almakhwah, Al Baha 1988, Saudi Arabia
| | - Ahmed Abdelsadik
- Zoology Department, Faculty of Science, Aswan University, Aswan 81528, Egypt;
| | - Ayman A. Saleh
- Department of Animal Wealth Development, Genetics and Genetic Engineering, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Ehab Kotb Elmahallawy
- Department of Biomedical Sciences, University of Leon, 24071 León, Spain
- Department of Zoonoses, Faculty of Veterinary Medicine, Sohag University, Sohag 82524, Egypt
| |
Collapse
|
282
|
Yang X, Zhao P, Dong Y, Chen S, Shen H, Jiang G, Zhu H, Dong J, Gao S. An isothermal recombinase polymerase amplification and lateral flow strip combined method for rapid on-site detection of Vibrio vulnificus in raw seafood. Food Microbiol 2020; 98:103664. [PMID: 33875195 DOI: 10.1016/j.fm.2020.103664] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023]
Abstract
Vibrio vulnificus is an important foodborne pathogenic bacterium that mainly contaminates seafood. Rapid and accurate technologies that suitable for on-site detection are critical for effective control of its spreading. Conventional detection methods and polymerase chain reaction (PCR)-based and qPCR-based approaches have application limitations in on-site scenarios. Application of loop-mediated isothermal amplification (LAMP) technology was a good step towards the on-site detection. In this study, a recombinase polymerase amplification (RPA)-based detection method for V. vulnificus was developed combining with lateral flow strip (LFS) for visualized signal. The method targeted the conservative empV gene encoding the extracellular metalloproteinase, and finished detection in 35 min at a conveniently low temperature of 37 °C. It showed good specificity and an excellent sensitivity of 2 copies of the genome or 10-1 colony forming unit (CFU) per reaction, or 1 CFU/10 g in spiked food samples with enrichment. The method tolerated unpurified templates directly from sample boiling, which added the convenience of the overall procedure. Application of the RPA-LFS method for clinical samples showed accurate and consistent detection results compared to bioassay and quantitative PCR. This RPA-LFS combined method is well suited for on-site detection of V. vulnificus.
Collapse
Affiliation(s)
- Xiaohan Yang
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Panpan Zhao
- Key Laboratory of Zoonosis Research By Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Yu Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Shiqi Chen
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Hui Shen
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, 226007, China
| | - Ge Jiang
- Jiangsu Institute of Oceanology and Marine Fisheries, Nantong, 226007, China
| | - Hai Zhu
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jingquan Dong
- Jiangsu Key Laboratory of Marine Biological Resources and Environment, Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China.
| | - Song Gao
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China.
| |
Collapse
|
283
|
Suea-Ngam A, Bezinge L, Mateescu B, Howes PD, deMello AJ, Richards DA. Enzyme-Assisted Nucleic Acid Detection for Infectious Disease Diagnostics: Moving toward the Point-of-Care. ACS Sens 2020; 5:2701-2723. [PMID: 32838523 PMCID: PMC7485284 DOI: 10.1021/acssensors.0c01488] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/25/2020] [Indexed: 02/08/2023]
Abstract
Driven by complex and interconnected factors, including population growth, climate change, and geopolitics, infectious diseases represent one of the greatest healthcare challenges of the 21st century. Diagnostic technologies are the first line of defense in the fight against infectious disease, providing critical information to inform epidemiological models, track diseases, decide treatment choices, and ultimately prevent epidemics. The diagnosis of infectious disease at the genomic level using nucleic acid disease biomarkers has proven to be the most effective approach to date. Such methods rely heavily on enzymes to specifically amplify or detect nucleic acids in complex samples, and significant effort has been exerted to harness the power of enzymes for in vitro nucleic acid diagnostics. Unfortunately, significant challenges limit the potential of enzyme-assisted nucleic acid diagnostics, particularly when translating diagnostic technologies from the lab toward the point-of-use or point-of-care. Herein, we discuss the current state of the field and highlight cross-disciplinary efforts to solve the challenges associated with the successful deployment of this important class of diagnostics at or near the point-of-care.
Collapse
Affiliation(s)
- Akkapol Suea-Ngam
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Léonard Bezinge
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Bogdan Mateescu
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
- Brain Research Institute,
Medical Faculty of the University of
Zürich, Winterthurerstrasse 190, 8057
Zürich, Switzerland
| | - Philip D. Howes
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Andrew J. deMello
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| | - Daniel A. Richards
- Institute for Chemical &
Bioengineering, Department of Chemistry & Applied Biosciences,
ETH Zürich,
Vladimir-Prelog-Weg 1, 8093 Zürich,
Switzerland
| |
Collapse
|
284
|
Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria. Proc Natl Acad Sci U S A 2020; 117:25722-25731. [PMID: 32958655 PMCID: PMC7568265 DOI: 10.1073/pnas.2010196117] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Detection of submicroscopic malaria in asymptomatic individuals is needed for eradication and remains a diagnostic gap in resource-limited settings. Nonfalciparum clinical diagnostics are a second gap, as these infections have a low parasite density and are commonly undetected. We describe an integrated, 60-min, ultrasensitive and specific CRISPR-based diagnostic for the four major pathogenic Plasmodium species that can fill these gaps. Using the SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform, we designed assays with limits of detection below that recommended by the World Health Organization. These assays have a simplified sample preparation method: the SHERLOCK parasite rapid extraction protocol, which eliminates complicated nucleic acid extraction steps. Our work further translates the SHERLOCK platform into a field-deployable diagnostic. Asymptomatic carriers of Plasmodium parasites hamper malaria control and eradication. Achieving malaria eradication requires ultrasensitive diagnostics for low parasite density infections (<100 parasites per microliter blood) that work in resource-limited settings (RLS). Sensitive point-of-care diagnostics are also lacking for nonfalciparum malaria, which is characterized by lower density infections and may require additional therapy for radical cure. Molecular methods, such as PCR, have high sensitivity and specificity, but remain high-complexity technologies impractical for RLS. Here we describe a CRISPR-based diagnostic for ultrasensitive detection and differentiation of Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale, and Plasmodium malariae, using the nucleic acid detection platform SHERLOCK (specific high-sensitivity enzymatic reporter unlocking). We present a streamlined, field-applicable, diagnostic comprised of a 10-min SHERLOCK parasite rapid extraction protocol, followed by SHERLOCK for 60 min for Plasmodium species-specific detection via fluorescent or lateral flow strip readout. We optimized one-pot, lyophilized, isothermal assays with a simplified sample preparation method independent of nucleic acid extraction, and showed that these assays are capable of detection below two parasites per microliter blood, a limit of detection suggested by the World Health Organization. Our P. falciparum and P. vivax assays exhibited 100% sensitivity and specificity on clinical samples (5 P. falciparum and 10 P. vivax samples). This work establishes a field-applicable diagnostic for ultrasensitive detection of asymptomatic carriers as well as a rapid point-of-care clinical diagnostic for nonfalciparum malaria species and low parasite density P. falciparum infections.
Collapse
|
285
|
Yasukawa K, Yanagihara I, Fujiwara S. Alteration of enzymes and their application to nucleic acid amplification (Review). Int J Mol Med 2020; 46:1633-1643. [PMID: 33000189 PMCID: PMC7521554 DOI: 10.3892/ijmm.2020.4726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of polymerase chain reaction (PCR) in 1985, several methods have been developed to achieve nucleic acid amplification, and are currently used in various fields including clinical diagnosis and life science research. Thus, a wealth of information has accumulated regarding nucleic acid-related enzymes. In this review, some nucleic acid-related enzymes were selected and the recent advances in their modification along with their application to nucleic acid amplification were described. The discussion also focused on optimization of the corresponding reaction conditions. Using newly developed enzymes under well-optimized reaction conditions, the sensitivity, specificity, and fidelity of nucleic acid tests can be improved successfully.
Collapse
Affiliation(s)
- Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606‑8502, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi, Osaka 594‑1101, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei‑Gakuin University, Sanda, Hyogo 669‑1337, Japan
| |
Collapse
|
286
|
P.E. S, Miller TS, Meng L, Unwin PR, Macpherson JV. Quantitative trace level voltammetry in the presence of electrode fouling agents: Comparison of single-walled carbon nanotube network electrodes and screen-printed carbon electrodes. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
287
|
Abstract
Ubiquitous post-transcriptional regulators in eukaryotes, microRNAs are currently emerging as promising biomarkers of physiological and pathological processes. Multiplex and digital detection of microRNAs represents a major challenge toward the use of microRNA signatures in clinical settings. The classical reverse transcription polymerase chain reaction quantification approach has important limitations because of the need for thermocycling and a reverse transcription step. Simpler, isothermal alternatives have been proposed, yet none could be adapted in both a digital and multiplex format. This is either because of a lack of sensitivity that forbids single molecule detection or molecular cross-talk reactions that are responsible for nonspecific amplification. Building on an ultrasensitive isothermal amplification mechanism, we present a strategy to suppress cross-talk reactions, allowing for robust isothermal and multiplex detection of microRNA targets. Our approach relies on target-specific DNA circuits interconnected with DNA-encoded inhibitors that repress nonspecific signal amplification. We demonstrate the one-step, isothermal, digital, and simultaneous quantification of various pairs of important microRNA targets.
Collapse
Affiliation(s)
- Yannick Rondelez
- Gulliver Laboratory, ESPCI Paris—Université PSL, 10 rue Vauquelin, 75005 Paris, France
| | - Guillaume Gines
- Gulliver Laboratory, ESPCI Paris—Université PSL, 10 rue Vauquelin, 75005 Paris, France
| |
Collapse
|
288
|
Zhang J, Liu J, An D, Fan Y, Cheng Z, Tang Y, Diao Y. A novel recombinase polymerase amplification assay for rapid detection of epidemic fowl adenovirus. Poult Sci 2020; 99:6446-6453. [PMID: 33248559 PMCID: PMC7449135 DOI: 10.1016/j.psj.2020.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 07/28/2020] [Accepted: 08/15/2020] [Indexed: 11/30/2022] Open
Abstract
Fowl adenovirus (FAdV) has posed a grave threat to the health of poultry, and the sudden outbreak highlights the importance of the new rapid diagnostic method for the control and prevention of transmission. Hence, in the present study, a novel recombinase polymerase amplification (RPA) assay, which was suitable for all 12 serotypes (FAdV-1 to 8a and 8b to 11) had been successfully launched to detect FAdV. Also, the entire amplification process could be completed in the isothermal condition when temperature ranged from 26 to 42°C within no more than 14 min, which was remarkably superior to endpoint polymerase chain reaction (98 min) with the same detecting sensitivity (as low as 0.1 fg viral DNA), avoiding sophisticated thermal cyclers with simple operation. Additionally, the same primers did not produce positive reactions with other viruses tested, demonstrating that the specificity of the RPA assay was acceptable. Moreover, this developed method could be efficiently used in the diagnosis of FAdV references and epidemic strains from different avian origins, thus making it a rapid, reliable, and point-of-care FAdV diagnostics tool, as well as an alternative to endpoint PCR.
Collapse
Affiliation(s)
- Ji Zhang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jie Liu
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Da An
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yunhao Fan
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Ziqiang Cheng
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
| |
Collapse
|
289
|
Kilic T, Weissleder R, Lee H. Molecular and Immunological Diagnostic Tests of COVID-19: Current Status and Challenges. iScience 2020; 23:101406. [PMID: 32771976 PMCID: PMC7381402 DOI: 10.1016/j.isci.2020.101406] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022] Open
Abstract
Rapid spread of coronavirus disease 2019 (COVID-19) is ravaging the globe. Since its first report in December 2019, COVID-19 cases have exploded to over 14 million as of July 2020, claiming more than 600,000 lives. Implementing fast and widespread diagnostic tests is paramount to contain COVID-19, given the current lack of an effective therapeutic or vaccine. This review focuses on a broad description of currently available diagnostic tests to detect either the virus (SARS-CoV-2) or virus-induced immune responses. We specifically explain the working mechanisms of these tests and compare their analytical performance. These analyses will assist in selecting most effective tests for a given application, for example, epidemiology or global pandemic research, population screening, hospital-based testing, home-based and point-of-care testing, and therapeutic trials. Finally, we lay out the shortcomings of certain tests and future needs.
Collapse
Affiliation(s)
- Tugba Kilic
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA 02114 USA
| | - Ralph Weissleder
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA 02114 USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hakho Lee
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA 02114 USA.
| |
Collapse
|
290
|
RPA-PCR couple: an approach to expedite plant diagnostics and overcome PCR inhibitors. Biotechniques 2020; 69:270-280. [PMID: 32815734 DOI: 10.2144/btn-2020-0065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA extraction can be lengthy and sometimes ends up with amplification inhibitors. We present the potential of recombinase polymerase amplification (RPA) to replace plant DNA extraction. In our rapid 'RPA-PCR couple' concept, RPA is tuned to slower reaction kinetics to promote amplification of long targets. RPA primers amplify target and some flanking regions directly from simple plant macerates. Then PCR primers exponentially amplify the target directly from the RPA reaction. We present the coupling of RPA with conventional, TaqMan and SYBR Green PCR assays. We applied the concept to strawberry Phytophthora pathogens and the Phytophthora identification marker atp9-nad9. We found RPA-PCR couple specific, sensitive and reliable. The approach may also benefit other difficult samples such as food, feces and ancient samples.
Collapse
|
291
|
Behrmann O, Bachmann I, Spiegel M, Schramm M, Abd El Wahed A, Dobler G, Dame G, Hufert FT. Rapid Detection of SARS-CoV-2 by Low Volume Real-Time Single Tube Reverse Transcription Recombinase Polymerase Amplification Using an Exo Probe with an Internally Linked Quencher (Exo-IQ). Clin Chem 2020; 66:1047-1054. [PMID: 32384153 PMCID: PMC7239256 DOI: 10.1093/clinchem/hvaa116] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/05/2020] [Indexed: 01/22/2023]
Abstract
Background The current outbreak of SARS-CoV-2 has spread to almost every country with more than three million confirmed cases and over two hundred thousand deaths as of April 28, 2020. Rapid first-line testing protocols are needed for outbreak control and surveillance. Methods We used computational and manual design to generate a suitable set of reverse transcription recombinase polymerase amplification (RT-RPA) primer and exonuclease probe, internally quenched (exo-IQ) probe sequences targeting the SARS-CoV-2 N gene. RT-RPA sensitivity was determined by amplification of in vitro transcribed RNA standards. Assay selectivity was demonstrated with a selectivity panel of 32 nucleic acid samples derived from common respiratory viruses. To validate the assay against full-length SARS-CoV-2 RNA, total viral RNA derived from cell culture supernatant and 19 nasopharyngeal swab samples (8 positive and 11 negative for SARS-CoV-2) were screened. All results were compared to established RT-qPCR assays. Results The 95% detection probability of the RT-RPA assay was determined to be 7.74 (95% CI: 2.87 - 27.39) RNA copies per reaction. The assay showed no cross-reactivity to any other screened coronaviruses or respiratory viruses of clinical significance. The developed RT-RPA assay produced 100% diagnostic sensitivity and specificity when compared to RT-qPCR (n=20). Conclusion With a run time of 15 to 20 minutes and first results being available in under 7 minutes for high RNA concentrations, the reported assay constitutes one of the fastest nucleic acid based detection methods for SARS-CoV-2 to date and may provide a simple to use alternative to RT-qPCR for first-line screening at the point of need.
Collapse
Affiliation(s)
- Ole Behrmann
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Iris Bachmann
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Martin Spiegel
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Marina Schramm
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, University of Göttingen, Germany.,Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany
| | - Gerhard Dobler
- Bundeswehr Institute of Microbiology (IMB), Munich, Germany
| | - Gregory Dame
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Frank T Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Fontane, Neuruppin, Germany.,Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| |
Collapse
|
292
|
Zhu Y, Zeng F, Sun J, Liu X, Wu M, Huang B, Lian Y, Xiao L, Ma L, Zhang S, Cong F. Application of recombinase polymerase amplification method for rapid detection of infectious laryngotracheitis virus. Mol Cell Probes 2020; 54:101646. [PMID: 32758643 DOI: 10.1016/j.mcp.2020.101646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/24/2020] [Accepted: 08/01/2020] [Indexed: 11/16/2022]
Abstract
Infectious laryngotracheitis is a significant respiratory disease of chickens that causes huge economic losses due to high morbidity and mortality and reduced egg production. A real-time recombinase polymerase amplification (RPA) assay was developed to accurately detect ILTV. The specific probe and primer sets were carefully designed and screened. The real-time RPA assay was carried out at 39 °C for 30 min, and results were obtained within 15 min. The results of the specificity assay showed no fluorescence signals with other avian-related viruses. The sensitivity of the assay was 1 × 102 copies/μL. The low CV value showed that the assay was reproducible. A total of 115 clinical samples were tested using the real-time RPA assay and the real-time PCR assay in parallel; the coincidence rates of the two detection methods were 100%. The results indicated that the real-time RPA assay is a specific, sensitive, rapid, and useful tool for epidemiological studies and clinical diagnosis, especially in the field and in resource-poor areas.
Collapse
Affiliation(s)
- Yujun Zhu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Fanwen Zeng
- College of Animal Science, South China Agricultural University, Wushan Road 483, Tianhe District, Guangzhou, 510642, China
| | - Junying Sun
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangdong Open Laboratory of Veterinary Public Health, Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Guangzhou, 510640, Guangdong, China
| | - Xiangnan Liu
- College of Animal Science and Technology, Guangdong Polytechnic of Science and Trade, Guangzhou, 510640, China
| | - Miaoli Wu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Bihong Huang
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Yuexiao Lian
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Li Xiao
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Lei Ma
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China
| | - Shouquan Zhang
- College of Animal Science, South China Agricultural University, Wushan Road 483, Tianhe District, Guangzhou, 510642, China.
| | - Feng Cong
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| |
Collapse
|
293
|
Xu H, Zhang X, Cai Z, Dong X, Chen G, Li Z, Qiu L, He L, Liang B, Liu X, Liu J. An Isothermal Method for Sensitive Detection of Mycobacterium tuberculosis Complex Using Clustered Regularly Interspaced Short Palindromic Repeats/Cas12a Cis and Trans Cleavage. J Mol Diagn 2020; 22:1020-1029. [PMID: 32470556 DOI: 10.1016/j.jmoldx.2020.04.212] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/13/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis is one of the most serious infectious diseases, resulting in death worldwide. Traditional detection methods are not enough to meet the clinical requirements of rapid diagnosis, high specificity, and high sensitivity. Fast, sensitive, and accurate detection of Mycobacterium tuberculosis (MTB) is urgently needed to treat and control tuberculosis disease. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas12a) exhibit strong nonspecific degradation ability of exogenous single-strand nucleic acids (trans cleavage) after specific recognition of target sequence. We purified Cas12a protein and selected a proper guide RNA based on conserved sequences of MTB from designed guide RNA library. Then, we proposed a novel detection method based on recombinase polymerase amplification and CRISPR/Cas12a nuclease system for specific and sensitive detection of MTB DNA. The assay, based on fluorescence detection, showed 4.48 fmol/L of limit of detection and good linear correlation of concentration with fluorescence value (R2 = 0.9775). It also showed good performance in distinguishing other bacteria. Furthermore, its clinical performance was evaluated by 193 samples and showed sensitivity of 99.29% (139/140) and specificity of 100% (53/53) at 99% CI, compared with culture method. Taken together, the CRISPR/Cas12a system showed good specificity, excellent sensitivity, and excellent accuracy for MTB detection, and it meets requirements of MTB detection in clinical samples and has great potential for clinical translation.
Collapse
Affiliation(s)
- Haipo Xu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Xiaolong Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Xiuqing Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Liman Qiu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China
| | - Lei He
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, People's Republic of China
| | - Bin Liang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, People's Republic of China.
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, People's Republic of China; Mengchao Med-X Center, Fuzhou University, Fuzhou, People's Republic of China; Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| |
Collapse
|
294
|
Heeroma AJ, Gwenin C. Development of Solid-Phase RPA on a Lateral Flow Device for the Detection of Pathogens Related to Sepsis. SENSORS (BASEL, SWITZERLAND) 2020; 20:E4182. [PMID: 32731402 PMCID: PMC7436017 DOI: 10.3390/s20154182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
Population extended life expectancy has significantly increased the risk of septic shock in an ageing population. Sepsis affects roughly 20 million people every year, resulting in over 11 million deaths. The need for faster more accurate diagnostics and better management is therefore paramount in the fight to prevent these avoidable deaths. Here we report the development of a POC device with the ability to identify a broad range of pathogens on a lateral flow platform. Namely Gram-positive and Gram-negative bacteria. The simple to use laboratory device has the potential to be automated, thus enabling an operator to carry out solid-phase lysis and room temperature RPA in situ, providing accurate results in hours rather than days. Results show there is a potential for a fully automated device in which concepts described in this paper can be integrated into a lateral flow device.
Collapse
Affiliation(s)
- Alice Jane Heeroma
- School of Natural Sciences, Bangor University, post code Bangor, Gwynedd, Wales LL57 2UW, UK;
| | - Christopher Gwenin
- School of Natural Sciences, Bangor University, post code Bangor, Gwynedd, Wales LL57 2UW, UK;
- Department of Chemistry, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou Industrial Park, Suzhou 215123, China
| |
Collapse
|
295
|
Han Y, Wang J, Zhang S, Wang J, Qin C, Han Y, Xu X. Rapid detection of norovirus genogroup II in clinical and environmental samples using recombinase polymerase amplification. Anal Biochem 2020; 605:113834. [PMID: 32712062 DOI: 10.1016/j.ab.2020.113834] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022]
Abstract
Norovirus is the leading cause of acute gastroenteritis all over the world, and the most genotype that causes its epidemic is norovirus genogroup II (NoVs GII). Rapid detection of NoVs is important because it can facilitate timely diagnosis. In this study, we designed universal specific primers and an Exo probe to hybridize to all genetic clusters of NoVs GII based on the conserved region at the ORF1-ORF2 junction of the genome. For the first time, we established a rapid and reliable reverse transcription recombinase polymerase amplification (RT-RPA) method for the detection of NoVs GII within 20 min. This method can specifically amplify NoVs GII, and the detection limit was as low as 1.66 × 102 copies/μL. The method was validated in terms of LOD, accuracy, and specificity. We tested 55 real samples including foods, water, and feces. The results showed a sensitivity of 96% and specificity of 100% to NoVs GII. The whole procedure can be operated by a mobile suitcase laboratory, which is useful for resource-limited diagnostic laboratories. This novel real-time RT-RPA assay is an accurate tool for point-of-care testing of NoVs, providing practical support for norovirus-caused disease diagnosis and prevention.
Collapse
Affiliation(s)
- Yanzhen Han
- School of Public Health, And Key Laboratory of Environment and Human Health of Hebei Medical University, Shijiazhuang, 050017, China
| | - Jianchang Wang
- Technology Center of Shijiazhuang Customs, Shijiazhuang, 050051, China
| | - Shuhong Zhang
- Microbiological Laboratory, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, 050021, China
| | - Jinfeng Wang
- Technology Center of Shijiazhuang Customs, Shijiazhuang, 050051, China
| | - Chen Qin
- Clinical Laboratory of Hebei General Hospital, Shijiazhuang, 050051, China
| | - Yanqing Han
- Microbiological Laboratory, Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, 050021, China
| | - Xiangdong Xu
- School of Public Health, And Key Laboratory of Environment and Human Health of Hebei Medical University, Shijiazhuang, 050017, China.
| |
Collapse
|
296
|
Molecular Markers for Detecting Schistosoma Species by Loop-Mediated Isothermal Amplification. DISEASE MARKERS 2020; 2020:8042705. [PMID: 32774514 PMCID: PMC7396120 DOI: 10.1155/2020/8042705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/20/2020] [Accepted: 07/01/2020] [Indexed: 02/01/2023]
Abstract
Schistosomiasis is considered a neglected parasitic disease. Around 280,000 people die from it annually, and more than 779 million people are at risk of getting infected. The schistosome species which infect human beings are Schistosoma mansoni, Schistosoma haematobium, Schistosoma intercalatum, Schistosoma japonicum, Schistosoma guineensis, and Schistosoma mekongi. This disease is also of veterinary significance; the most important species being Schistosoma bovis since it causes the disease in around 160 million livestock in Africa and Asia. This work was aimed at designing and developing a genus-specific loop-mediated isothermal amplification (LAMP) method for detecting the most important schistosome species affecting humans and for the species-specific detection of S. bovis. Bioinformatics tools were used for primer design, and the LAMP method was standardised for detecting the ITS-1 region from S. intercalatum, S. haematobium, S. mansoni, S. japonicum, and S. bovis DNA (generic test) and the NADH 1 gene for specifically detecting S. bovis (at different DNA concentrations). Detection limits achieved were 1 pg DNA for S. mansoni, 0.1 pg for S. haematobium, 1 pg for S. intercalatum, and 10 pg for S. bovis. No amplification for S. japonicum DNA was obtained. The LAMP designed for the amplification of S. bovis NADH-1 worked specifically for this species, and no other DNA from other schistosome species included in the study was amplified. Two highly sensitive LAMP methods for detecting different Schistosoma species important for human and veterinary health were standardised. These methods could be very useful for the diagnosis and surveillance of schistosome infections.
Collapse
|
297
|
Fan X, Li L, Zhao Y, Liu Y, Liu C, Wang Q, Dong Y, Wang S, Chi T, Song F, Sun C, Wang Y, Ha D, Zhao Y, Bao J, Wu X, Wang Z. Clinical Validation of Two Recombinase-Based Isothermal Amplification Assays (RPA/RAA) for the Rapid Detection of African Swine Fever Virus. Front Microbiol 2020; 11:1696. [PMID: 32793160 PMCID: PMC7385304 DOI: 10.3389/fmicb.2020.01696] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
African swine fever (ASF), caused by African swine fever virus (ASFV), is a devastating infectious disease of domestic pigs and wild boars, and has tremendous negative socioeconomic impact on the swine industry and food security worldwide. It is characterized as a notifiable disease by World Organisation for Animal Health (OIE). No effective vaccine or treatment against ASF has so far been available. Early detection and rapid diagnosis are of potential significance to control the spread of ASF. Recombinase-based isothermal amplification assay, recombinase polymerase amplification (RPA) developed by TwistDx (Cambridge, United Kingdom) or recombinase-aided amplification (RAA) by Qitian (Wuxi, China), is becoming a molecular tool for the rapid, specific, and cost-effective identification of multiple pathogens. In this study, we aim to investigate if RPA/RAA can be a potential candidate for on-site, rapid and primary detection of ASFV. A panel of 152 clinical samples previously well-characterized by OIE-recommended qPCR was enrolled in this study, including 20 weak positive (Ct value ≥ 30) samples. This panel was consisted of different types, such as EDTA-blood, spleen, lung, lymph node, kidney, tonsil, liver, brain. We evaluated two recombinase-based isothermal amplification assays, RPA or RAA, by targeting the ASFV B646L gene (p72), and validated the clinical performance in comparison with OIE real-time PCR. Our result showed that the analytical sensitivity of RPA and RAA was as 93.4 and 53.6 copies per reaction, respectively at 95% probability in 16 min, at 39°C. They were universally specific for all 24 genotypes of ASFV and no cross reaction to other pathogens including Classical swine fever virus (CSV), Foot-and-mouth disease virus (FMDV), Pseudorabies virus, Porcine circovirus 2 (PCV2), Porcine Reproductive and respiratory syndrome virus (PPRSV). The results on detection of various kinds of clinical samples indicated an excellent diagnostic agreement between RPA, RAA and OIE real-time PCR method, with the kappa value of 0.960 and 0.973, respectively. Compared to real-time PCR, the specificity of both RPA and RAA was 100% (94.40% ∼ 100%, 95% CI), while the sensitivity was 96.59% (90.36% ∼ 99.29%, 95% CI) and 97.73% (92.03% ∼ 99.72%, 95% CI), respectively. Our data demonstrate that the developed recombinase-based amplification assay (RPA/RAA), promisingly equipped with field-deployable instruments, offers a sensitive and specific platform for the rapid and reliable detection of ASFV, especially in the resource-limited settings for the purpose of screening and surveillance of ASF.
Collapse
Affiliation(s)
- Xiaoxu Fan
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Lin Li
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yonggang Zhao
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yutian Liu
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Chunju Liu
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Qinghua Wang
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yaqin Dong
- Livestock Disease Surveillance Laboratory, China Animal Health and Epidemiology Center, Qingdao, China
| | - Shujuan Wang
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Tianying Chi
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Fangfang Song
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Chengyou Sun
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yingli Wang
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Dengchuriya Ha
- Vocational and Technical College, Inner Mongolia Agricultural University, Hohhot, China
| | - Yang Zhao
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China.,College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
| | - Jingyue Bao
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiaodong Wu
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| | - Zhiliang Wang
- National Reference Laboratory for African Swine Fever, National Surveillance and Research Center for Exotic Animal Diseases, National Surveillance and Research Center for Exotic Animal Diseases, China Animal Health and Epidemiology Center, Qingdao, China
| |
Collapse
|
298
|
El-Tholoth M, Mauk MG, Anis E, Bau HH. A closed-tube, single-step, real time, reverse transcription-loop-mediated isothermal amplification assay for infectious bronchitis virus detection in chickens. J Virol Methods 2020; 284:113940. [PMID: 32687868 PMCID: PMC7367007 DOI: 10.1016/j.jviromet.2020.113940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/24/2022]
Abstract
A closed tube, single-step-real-time-RT-LAMP assay was developed for detection and semi-quantification of IBV in closed tube. The least limit of detection of our assay is 1 EID50/ ml. Clinical evaluation of samples from diseased chickens using our assay shows a very good concordance with RT-qPCR assay.
Infectious bronchitis (IB) is a viral infection of the chicken respiratory tract that causes substantial economic burden on the industry. Simple, specific and rapid diagnosis of this disease is critical for the initiation of appropriate control measures. Conventional molecular diagnostic methods require a relatively sophisticated equipment and skilled staff. Here we describe a rapid, simple, semi-quantative, closed-tube, single-step, real-time- reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for IB and compare our assay with quantative, reverse transcription- polymerase chain reaction (RT-qPCR). The limit of detection (LOD) of our RT-LAMP assay is 1 EID50/ ml. Clinical evaluation of samples from diseased chickens with our RT-LAMP showed a very good concordance with RT-qPCR. Our assay enables simple, specific, rapid molecular detection and semi-quantification of the infectious bronchitis virus (IBV) in veterinary diagnostic laboratories. Furthermore, our RT-LAMP detection is carried out in a sealed tube, eliminating the risk of false-positive results in subsequent tests because of any contamination of the work area as in the case of lateral flow strip or gel electrophoresis-based amplicon detection.
Collapse
Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Michael G Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eman Anis
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA 19348, United States
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States
| |
Collapse
|
299
|
Yu F, Yuan Z, Zhang D, Liu Y, Zhao Q, Wang H. High-affinity and undissociated capillary electrophoresis for DNA strand exchange analysis. Chem Commun (Camb) 2020; 56:7403-7406. [PMID: 32514506 DOI: 10.1039/d0cc02844d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
By identification of a super-stable protein-DNA-affinity system, we developed a free-solution capillary electrophoresis approach for rapid and sensitive detection of fundamentally important DNA strand exchange reactions mediated by recombinases. We further extended this assay for identification of hyper-recombinases generated from bioengineering and detection of single DNA mismatches caused by replication error.
Collapse
Affiliation(s)
- Fangzhi Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, No. 18 Shuangqing Road, Beijing 100085, P. R. China.
| | | | | | | | | | | |
Collapse
|
300
|
Chen J, Jiang F, Huang CW, Lin L. Rapid genotypic antibiotic susceptibility test using CRISPR-Cas12a for urinary tract infection. Analyst 2020; 145:5226-5231. [PMID: 32597917 DOI: 10.1039/d0an00947d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The current clinical protocol to conduct a bacterial antibiotic susceptibility test (AST) requires at least 18 hours, and cannot be accomplished during a single visit for patients. Here, a new method based on the technique of CRISPR-Cas12a is utilized to accomplish a bacterial genotypic AST within one hour with good accuracy. Two amplification approaches are employed and compared: (1) enriching the bacterial concentration by culturing in growth media; and (2) amplifying target DNA from raw samples by recombinase polymerase amplification (RPA). The results show that CRISPR combined with RPA can rapidly and accurately provide a bacterial genotypic AST of urine samples with urinary tract infections for precise antibiotic treatment. As such, this technology could open a new class of rapid bacterial genotypic AST for various infectious diseases.
Collapse
Affiliation(s)
- Juhong Chen
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94760, USA.
| | | | | | | |
Collapse
|