1
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Dong Y, Zhou D, Zhang B, Xu X, Zhang J. Development of a real-time recombinase-aided amplification assay for rapid and sensitive detection of Edwardsiella piscicida. Front Cell Infect Microbiol 2024; 14:1355056. [PMID: 38606294 PMCID: PMC11007066 DOI: 10.3389/fcimb.2024.1355056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024] Open
Abstract
Edwardsiella piscicida, a significant intracellular pathogen, is widely distributed in aquatic environments and causes systemic infection in various species. Therefore, it's essential to develop a rapid, uncomplicated and sensitive method for detection of E. piscicida in order to control the transmission of this pathogen effectively. The recombinase-aided amplification (RAA) assay is a newly developed, rapid detection method that has been utilized for various pathogens. In the present study, a real-time RAA (RT-RAA) assay, targeting the conserved positions of the EvpP gene, was successfully established for the detection of E. piscicida. This assay can be performed in a one-step single tube reaction at a temperature of 39°C within 20 min. The RT-RAA assay exhibited a sensitivity of 42 copies per reaction at a 95% probability, which was comparable to the sensitivity of real-time quantitative PCR (qPCR) assay. The specificity assay confirmed that the RT-RAA assay specifically targeted E. piscicida without any cross-reactivity with other important marine bacterial pathogens. Moreover, when clinical specimens were utilized, a perfect agreement of 100% was achieved between the RT-RAA and qPCR assays, resulting a kappa value of 1. These findings indicated that the established RT-RAA assay provided a viable alternative for the rapid, sensitive, and specific detection of E. piscicida.
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Affiliation(s)
- Yuchen Dong
- School of Ocean, Yantai University, Yantai, China
| | - Dandan Zhou
- School of Ocean, Yantai University, Yantai, China
| | - Binzhe Zhang
- School of Ocean, Yantai University, Yantai, China
| | - Xiaoying Xu
- Yantai Marine Economic Research Institute, Yantai, China
| | - Jian Zhang
- School of Ocean, Yantai University, Yantai, China
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2
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Wang W, Wang B, Li Q, Tian R, Lu X, Peng Y, Sun J, Bai J, Gao Z, Sun X. Ultrasensitive Detection Strategy of Norovirus Based on a Dual Enhancement Strategy: CRISPR-Responsive Self-Assembled SNA and Isothermal Amplification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4415-4425. [PMID: 38355417 DOI: 10.1021/acs.jafc.4c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Spherical nucleic acids (SNAs) have been used to construct various nanobiosensors with gold nanoparticles (AuNPs) as nuclei. The SNAs play a critical role in biosensing due to their various physical and chemical properties, programmability, and specificity recognition ability. In this study, CRISPR-responsive self-assembled spherical nucleic acid (CRISPR-rsSNA) detection probes were constructed by conjugating fluorescein-labeled probes to the surface of AuNPs to improve the sensing performance. Also, the mechanism of ssDNA and the role of different fluorescent groups in the self-assembly process of CRISPR-rsSNA were explored. Then, CRISPR-rsSNA and reverse transcription-recombinase polymerase amplification (RT-RPA) were combined to develop an ultrasensitive fluorescence-detection strategy for norovirus. In the presence of the virus, the target RNA sequence of the virus was transformed and amplified by RT-RPA. The resulting dsDNA activated the trans-cleavage activity of CRISPR cas12a, resulting in disintegrating the outer nucleic acid structure of the CRISPR-rsSNA at a diffusible rate, which released reporter molecules. Norovirus was quantitated by fluorescence detection. This strategy facilitated the detection of the norovirus at the attomolar level. An RT-RPA kit for norovirus detected would be developed based on this method. The proposed method would be used for the detection of different viruses just by changing the target RNA and crRNA of the CRISPR cas12a system which provided a foundation for high-throughput detection of various substances.
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Affiliation(s)
- Weiya Wang
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Botao Wang
- School of Instrument Science and Optoelectronics Engineering, Beihang University, Beijing 100191, China
| | - Qiaofeng Li
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Run Tian
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Xin Lu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Jiadi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
| | - Jialei Bai
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, P.R. of China
| | - Xiulan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi 214122, Jiangsu, P. R. China
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3
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Trinh TND, Nam NN. Isothermal amplification-based microfluidic devices for detecting foodborne pathogens: a review. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1150-1157. [PMID: 38323529 DOI: 10.1039/d3ay02039h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The gold standard for nucleic acid amplification-based diagnosis is the polymerase chain reaction (PCR). The PCR recognizes the targets such as foodborne pathogens by amplifying their specific genes. The integration of nucleic acid amplification-based assays on microfluidic platforms represents a highly promising solution for convenient, cheap, and effective control of foodborne pathogens. However, the application of the PCR is limited to on-site detection because the method requires sophisticated equipment for temperature control, which makes it complicated for microfluidic integration. Alternatively, isothermal amplification methods are promising tools for integrating microfluidic platforms for on-site detection of foodborne pathogens. This review summarized advances in isothermal amplification-based microfluidic devices for detecting foodborne pathogens. Different nucleic acid extraction approaches and the integration of these approaches in microfluidic platforms were first reviewed. Microfluidic platforms integrated with three common isothermal amplification methods including loop-mediated isothermal amplification, recombinase polymerase amplification, and recombinase-aided amplification were then described and discussed.
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Affiliation(s)
- Thi Ngoc Diep Trinh
- Department of Materials Science, School of Applied Chemistry, Tra Vinh University, Tra Vinh City 87000, Vietnam.
| | - Nguyen Nhat Nam
- Applied Biology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
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4
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Ngoc LTN, Lee YC. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. BIOSENSORS 2024; 14:97. [PMID: 38392016 PMCID: PMC10886876 DOI: 10.3390/bios14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Ribonucleic acid (RNA) viruses are one of the major classes of pathogens that cause human diseases. The conventional method to detect RNA viruses is real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), but it has some limitations. It is expensive and time-consuming, with infrastructure and trained personnel requirements. Its high throughput requires sophisticated automation and large-scale infrastructure. Isothermal amplification methods have been explored as an alternative to address these challenges. These methods are rapid, user-friendly, low-cost, can be performed in less specialized settings, and are highly accurate for detecting RNA viruses. Microfluidic technology provides an ideal platform for performing virus diagnostic tests, including sample preparation, immunoassays, and nucleic acid-based assays. Among these techniques, nucleic acid isothermal amplification methods have been widely integrated with microfluidic platforms for RNA virus detection owing to their simplicity, sensitivity, selectivity, and short analysis time. This review summarizes some common isothermal amplification methods for RNA viruses. It also describes commercialized devices and kits that use isothermal amplification techniques for SARS-CoV-2 detection. Furthermore, the most recent applications of isothermal amplification-based microfluidic platforms for RNA virus detection are discussed in this article.
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Affiliation(s)
- Le Thi Nhu Ngoc
- Department of Nano Science and Technology Convergence, Gachon University, 1342 Seongnam-Daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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5
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Kim TY, Zhu X, Kim SM, Lim JA, Woo MA, Lim MC, Luo K. A review of nucleic acid-based detection methods for foodborne viruses: Sample pretreatment and detection techniques. Food Res Int 2023; 174:113502. [PMID: 37986417 DOI: 10.1016/j.foodres.2023.113502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 11/22/2023]
Abstract
Viruses are major pathogens that cause food poisoning when ingested via contaminated food and water. Therefore, the development of foodborne virus detection technologies that can be applied throughout the food distribution chain is essential for food safety. A common nucleic acid-based detection method is polymerase chain reaction (PCR), which has become the gold standard for monitoring food contamination by viruses due to its high sensitivity, and availability of commercial kits. However, PCR-based methods are labor intensive and time consuming, and are vulnerable to inhibitors that may be present in food samples. In addition, the methods are restricted with regard to site of analysis due to the requirement of expensive and large equipment for sophisticated temperature regulation and signal analysis procedures. To overcome these limitations, optical and electrical readout biosensors based on nucleic acid isothermal amplification technology and nanomaterials have emerged as alternatives for nucleic acid-based detection of foodborne viruses. Biosensors are promising portable detection tools owing to their easy integration into compact platforms and ability to be operated on-site. However, the complexity of food components necessitates the inclusion of tedious preprocessing steps, and the lack of stability studies on residual food components further restricts the practical application of biosensors as a universal detection method. Here, we summarize the latest advances in nucleic acid-based strategies for the detection of foodborne viruses, including PCR-based and isothermal amplification-based methods, gene amplification-free methods, as well as food pretreatment methods. The principles, strengths/disadvantages, and performance of each method, problems to be solved, and future prospects for the development of a universal detection method are discussed.
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Affiliation(s)
- Tai-Yong Kim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Xiaoning Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Se-Min Kim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea; Department of Food Science and Technology, Jeonbuk National University, Jeonju-si, Jeollabuk-do 54896, Republic of Korea
| | - Jeong-A Lim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Min-Ah Woo
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Min-Cheol Lim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea; Department of Food Biotechnology, Korea University of Science and Technology, Daejeon-si 34113, Republic of Korea.
| | - Ke Luo
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, China.
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Srivastava P, Prasad D. Human Norovirus Detection: How Much Are We Prepared? Foodborne Pathog Dis 2023; 20:531-544. [PMID: 37792418 DOI: 10.1089/fpd.2023.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Norovirus (NoV) is known to be the second nonbacterial enteric pathogen after rotavirus that causes acute gastroenteritis. They can be spread from person to person through fecal-oral routes. Infection can lead to severe diarrhea, causing stomach pain, vomiting, and nausea. Rapid detection of NoV can control huge economic and productive losses. Genotyping various emerging NoV strains is important to compare the severity among different strains. Conventional immunological and molecular methods have evolved and contributed to developing detection techniques. Immunological (enzyme-linked immunosorbent assay) and molecular detection (reverse transcriptase polymerase chain reaction [RT-PCR], RT-quantitative PCR, loop-mediated isothermal amplification, nucleic acid sequence-based alignment, recombinase polymerase amplification) methods have been mainly used. The development of biosensors using aptasensor, affinity peptides, nanoparticles, microfluidics, and so on, are currently the most researched topics. The availability of next-generation sequencing technologies has greatly influenced the diagnosis of NoV. The complementation of advanced technologies is helpful in identification of new variants. In this study, techniques that are useful in detecting NoV are discussed. This review has investigated the availability of recent methods used in the detection, present status, and futuristic plan of action in case of outbreak and pandemic.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India
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7
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Cao Y, Fang T, Shen J, Zhang G, Guo D, Zhao L, Jiang Y, Zhi S, Zheng L, Lv X, Yao Z, Yu D. Development of Recombinase Aided Amplification (RAA)-Exo-Probe Assay for the Rapid Detection of Shiga Toxin-Producing Escherichia coli. J AOAC Int 2023; 106:1246-1253. [PMID: 37252814 DOI: 10.1093/jaoacint/qsad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/11/2023] [Accepted: 05/20/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Shiga toxin-producing Escherichia coli (STEC) is a significant cause of foodborne illness causing various gastrointestinal diseases including hemolytic uremic syndrome (HUS), the most severe form, which can lead to kidney failure or even death. OBJECTIVE Here, we report the development of recombinase aided amplification (RAA)-exo-probe assays targeting the stx1 and stx2 genes for the rapid detection of STEC in food samples. METHODS Primers and exo-probes were designed and optimized for the detection of stx1 and stx2 using RAA technology. The optimal STEC RAA-exo-probe assays were then tested for specificity and sensitivity, and validated in both spiked and real food samples. RESULTS These assays were found to be 100% specific to STEC strains and were also highly sensitive with a detection limit of 1.6 × 103 CFU/mL or 32 copies/reaction. Importantly, the assays were able to successfully detect STEC in spiked and real food samples (beef, mutton, and pork), with a detection limit as low as 0.35 CFU/25g in beef samples after an overnight enrichment step. CONCLUSIONS Overall, the RAA assay reactions completed within ∼20 min and were less dependent on expensive equipment, suggesting they can be easily adopted for in-field testing requiring only a fluorescent reader. HIGHLIGHTS As such, we have developed two rapid, sensitive, and specific assays that can be used for the routine monitoring of STEC contamination in food samples, particularly in the field or in poorly equipped labs.
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Affiliation(s)
- Yuhao Cao
- Ningbo University, Health Science Center, 818 Fenghua Road, Jiangbei District, Ningbo 315211, China
| | - Taisong Fang
- Zhejiang University, College of Biosystems Engineering and Food Science, 866 Yuhangtang Road, Xihu District, Hangzhou 310058, China
| | - Jinling Shen
- Shanghai Customs, Technology Center for Animal Plant and Food Inspection and Quarantine, 299 Mianbei Road, Pudong New District, Shanghai 201210, China
| | - Guodong Zhang
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Drive, College Park, MD 20740, USA
| | - Dehua Guo
- Shanghai Customs, Technology Center for Animal Plant and Food Inspection and Quarantine, 299 Mianbei Road, Pudong New District, Shanghai 201210, China
| | - Lina Zhao
- Shanghai Customs, Technology Center for Animal Plant and Food Inspection and Quarantine, 299 Mianbei Road, Pudong New District, Shanghai 201210, China
| | - Yuan Jiang
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, 1 Weigang, Nanjing 210095, China
| | - Shuai Zhi
- Ningbo University, Health Science Center, 818 Fenghua Road, Jiangbei District, Ningbo 315211, China
| | - Lin Zheng
- Ningbo University, The First Affiliated Hospital of Ningbo University, 59 Liuting Street, Haishu District, Ningbo 315211, China
| | - Xiaofei Lv
- China Jiliang University, Department of Environmental Engineering, 258 Xueyuan Street, Qiantang District, Hangzhou 310018, China
| | - Zhiyuan Yao
- Ningbo University, School of Civil and Environmental Engineering, 818 Fenghua Road, Jiangbei District, Ningbo 315211, China
| | - Daniel Yu
- University of Alberta, School of Public Health, 116 Street and 85 Avenue, Edmonton, AB, Canada
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8
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Wang X, Dai C, Wu Y, Liu Y, Wei D. Molecular-electromechanical system for unamplified detection of trace analytes in biofluids. Nat Protoc 2023:10.1038/s41596-023-00830-x. [PMID: 37208410 DOI: 10.1038/s41596-023-00830-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/07/2023] [Indexed: 05/21/2023]
Abstract
Biological research and diagnostic applications normally require analysis of trace analytes in biofluids. Although considerable advancements have been made in developing precise molecular assays, the trade-off between sensitivity and ability to resist non-specific adsorption remains a challenge. Here, we describe the implementation of a testing platform based on a molecular-electromechanical system (MolEMS) immobilized on graphene field-effect transistors. A MolEMS is a self-assembled DNA nanostructure, containing a stiff tetrahedral base and a flexible single-stranded DNA cantilever. Electromechanical actuation of the cantilever modulates sensing events close to the transistor channel, improving signal-transduction efficiency, while the stiff base prevents non-specific adsorption of background molecules present in biofluids. A MolEMS realizes unamplified detection of proteins, ions, small molecules and nucleic acids within minutes and has a limit of detection of several copies in 100 μl of testing solution, offering an assay methodology with wide-ranging applications. In this protocol, we provide step-by-step procedures for MolEMS design and assemblage, sensor manufacture and operation of a MolEMS in several applications. We also describe adaptations to construct a portable detection platform. It takes ~18 h to construct the device and ~4 min to finish the testing from sample addition to result.
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Affiliation(s)
- Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Yungeng Wu
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China.
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China.
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9
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Li FY, Guo YH, Sun ZL, Liu H, Zhao MC, Cui J, Jiang Y, Shen XX, Ma XJ, Feng ZS. Rapid two-stage amplification in a single tube for simultaneous detection of norovirus GII and group a rotavirus. J Clin Lab Anal 2023; 37:e24858. [PMID: 36916770 PMCID: PMC10098066 DOI: 10.1002/jcla.24858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023] Open
Abstract
The most prevalent viruses currently causing diarrhea are norovirus and rotavirus, and rapid and sensitive detection methods are essential for the early diagnosis of disease. The purpose of this study was to establish a sensitive single-tube two-stage nucleic acid amplification method-reverse transcription recombinase-assisted PCR (RT-RAP)-for simultaneous detection of norovirus GII and group A Rotavirus, with the first stage consisting of isothermal reverse transcription recombinase-aided amplification (RT-RAA) and the second stage consisting of qPCR (quantitative PCR). RT-RAP is more sensitive than either RT-RAA or qRT-PCR (quantitative RT-PCR) alone. And the addition of a barrier that can be disassembled after heating enabled the detection of samples within 1 h in a single closed tube. Sensitivity was 10 copies/reaction of norovirus (Novs) GII and group A rotavirus (RVA). In parallel, two hundred fecal specimens were used to evaluate the method and compare it with a commercial fluorescent quantitative RT-PCR. The data showed kappa values of 0.957 and 0.98 (p < 0.05) for detecting Novs GII and RVA by the two methods, indicating the potential of the newly established assay to be applied to clinical and laboratory testing.
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Affiliation(s)
- Feng-Yu Li
- Hebei Medical University, Shijiazhuang, Hebei, China.,Hebei General Hospital, Shijiazhuang, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying-Hui Guo
- Department of Clinical Laboratory, Children's Hospital of Hebei Province, Shijiazhuang, Hebei, China
| | - Zhen-Lu Sun
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Meng-Chuan Zhao
- Department of Clinical Laboratory, Children's Hospital of Hebei Province, Shijiazhuang, Hebei, China
| | - Jia Cui
- Hebei General Hospital, Shijiazhuang, Hebei, China
| | - Yue Jiang
- The Third Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhi-Shan Feng
- Hebei Medical University, Shijiazhuang, Hebei, China.,Hebei General Hospital, Shijiazhuang, Hebei, China.,Hebei Medical Laboratory Clinical Medical Research Center, Shijiazhuang City, Hebei Province, China.,Hebei Key Laboratory of Molecular Medicine, Shijiazhuang City, Hebei Province, China
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10
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Cui X, Du B, Feng J, Feng Y, Cui J, Yan C, Zhao H, Gan L, Fan Z, Fu T, Xu Z, Zhang R, Du S, Zhou Y, Tian Z, Zhang Q, Fu H, Xue G, Yuan J. Rapid detection of mpox virus using recombinase aided amplification assay. Front Cell Infect Microbiol 2023; 13:1008783. [PMID: 36909721 PMCID: PMC9996015 DOI: 10.3389/fcimb.2023.1008783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
A recent, unprecedented outbreak of human mpox virus infection has led to cases in non-African nations, and the number of confirmed or suspected cases outside of Africa has exceeded 1,000 within 5 weeks. Mpox may pose a double threat to public health in the context of the ongoing COVID-19 pandemic. It is difficult to distinguish mpox virus infection from other diseases in the early stages, and patients are contagious from the onset of nonspecific symptoms; therefore, it is crucial to develop rapid and specific diagnostic methods. The diagnosis of mpox relies on real-time polymerase chain reaction, a time-consuming method that requires a highly sophisticated thermal cycler, which makes it unsuitable for widespread use in underdeveloped areas, where the outbreak is still severe. In this study, we developed a recombinase-aided amplification (RAA) assay that can detect mpox virus within 5-10 minutes. The conserved regions of the A27L gene and F3L gene were selected as targets, as they amplify well from different mpox virus clades with no cross-reaction from other pathogens. The sensitivity of this RAA assay is 10 copies/reaction for the A27L gene and 102 copies/reaction for the F3L gene. When applied to simulated clinical samples, both targets showed 100% specificity, and the detection limits were consistent with the sensitivity results. Moreover, through clinical blinded sample detection, RAA exhibits the same detection power as RT-PCR. In summary, the RAA mpox assay described here exhibits rapid detection, high sensitivity and specificity, and low operational difficulty, making it suitable for mpox virus detection in less developed countries and regions.
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Affiliation(s)
- Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yao Zhou
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Qun Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanyu Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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Gui L, Zhao Y, Xu D, Li X, Luo J, Zhou W, Li M. Quick detection of Carassius auratus herpesvirus (CaHV) by recombinase-aid amplification lateral flow dipstick (RAA-LFD) method. Front Cell Infect Microbiol 2022; 12:981911. [PMID: 36171755 PMCID: PMC9512145 DOI: 10.3389/fcimb.2022.981911] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/19/2022] [Indexed: 12/03/2022] Open
Abstract
Crucian carp (Carassius auratus) is one of the major freshwater species and is also a common food fish in China. Recently, Carassius auratus herpesvirus (CaHV) could induce fatal viral disease with high mortality of crucian carp, which had caused huge economic losses. In this study, we described a rapid and simple recombinase-aid amplification (RAA) assay coupled with lateral flow dipstick (LFD), which could achieve sensitive diagnosis of tumor necrosis factor receptor (TNFR) of CaHV within 35 min at 40°C. Our RAA-LFD method had a satisfactory detection limit of 100 gene copies per reaction, which was 100-fold more sensitive than traditional PCR. In addition, no cross-reaction was observed with other viral pathogens, including koi herpesvirus (KHV), cyprinid herpesvirus 2 (CyHV-2), infectious hematopoietic necrosis virus (IHNV), spring viremia of carp virus (SVCV) and grass carp reovirus (GCRV). Furthermore, the overall cost of the method was cut in half compared to previous studies. In conclusion, RAA-LFD assay is therefore, a promising alternative for point-of-care testing (POCT) of CaHV, which is feasible and of certain value in application of aquatic disease control.
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Affiliation(s)
- Lang Gui
- Key Laboratory of integrated rice-fish farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Yun Zhao
- Key Laboratory of integrated rice-fish farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Dan Xu
- Key Laboratory of integrated rice-fish farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Xinyu Li
- Key Laboratory of integrated rice-fish farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Jianhua Luo
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Wenzong Zhou
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Wenzong Zhou, ; Mingyou Li,
| | - Mingyou Li
- Key Laboratory of integrated rice-fish farming, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- *Correspondence: Wenzong Zhou, ; Mingyou Li,
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12
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Fu H, Gan L, Tian Z, Han J, Du B, Xue G, Feng Y, Zhao H, Cui J, Yan C, Feng J, Fan Z, Fu T, Xu Z, Zhang R, Cui X, Du S, Zhou Y, Zhang Q, Cao L, Yuan J. Rapid detection of Burkholderia cepacia complex carrying the 16S rRNA gene in clinical specimens by recombinase-aided amplification. Front Cell Infect Microbiol 2022; 12:984140. [PMID: 36132989 PMCID: PMC9483118 DOI: 10.3389/fcimb.2022.984140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
The Burkholderia cepacia complex (BCC) is a group of opportunistic pathogens, including Burkholderia cepacia, Burkholderia multivorans, Burkholderia vietnamiensis and Burkholderia ambifaria, which can cause severe respiratory tract infections and lead to high mortality rates among humans. The early diagnosis and effective treatment of BCC infection are therefore crucial. In this study, a novel and rapid recombinase-aided amplification (RAA) assay targeting the 16S rRNA gene was developed for BCC detection. The protocol for this RAA assay could be completed in 10 min at 39°C, with a sensitivity of 10 copies per reaction and no cross-reactivity with other pathogens. To characterize the effectiveness of the RAA assay, we further collected 269 clinical samples from patients with bacterial pneumonia. The sensitivity and specificity of the RAA assay were 100% and 98.5%, respectively. Seven BCC-infected patients were detected using the RAA assay, and three BCC strains were isolated from the 269 clinical samples. Our data showed that the prevalence of BCC infection was 2.60%, which is higher than the 1.40% reported in previous studies, suggesting that high sensitivity is vital to BCC detection. We also screened a patient with B. vietnamiensis infection using the RAA assay in clinic, allowing for appropriate treatment to be initiated rapidly. Together, these data indicate that the RAA assay targeting the 16S rRNA gene can be applied for the early and rapid detection of BCC pathogens in patients with an uncharacterized infection who are immunocompromised or have underlying diseases, thereby providing guidance for effective treatment.
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Affiliation(s)
- Hanyu Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- Department of Pulmonology, The Affiliated Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Juqiang Han
- Institute of Hepatology, Chinese People Liberation Army General Hospital, Beijing, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yao Zhou
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Qun Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ling Cao
- Department of Pulmonology, The Affiliated Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
- *Correspondence: Jing Yuan, ; Ling Cao,
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- *Correspondence: Jing Yuan, ; Ling Cao,
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13
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Abstract
INTRODUCTION Recombinase polymerase amplification (RPA) is a promising and emerging technology for rapidly amplifying target nucleic acid from minimally processed samples and through small portable instruments. RPA is suitable for point-of-care testing (POCT) and on-site field testing, and it is compatible with microfluidic devices. Several detection assays have been developed, but limited research has dug deeper into the chemistry of RPA to understand its kinetics and fix its shortcomings. AREAS COVERED This review provides a detailed introduction of RPA molecular mechanism, kits formats, optimization, application, pros, and cons. Moreover, this critical review discusses the nonspecificity issue of RPA, highlights its consequences, and emphasizes the need for more research to resolve it. This review discusses the reaction kinetics of RPA in relation to target length, product quantity, and sensitivity. This critical review also questions the novelty of recombinase-aided amplification (RAA). In short, this review discusses many aspects of RPA technology that have not been discussed previously and provides a deeper insight and new perspectives of the technology. EXPERT OPINION RPA is an excellent choice for pathogen detection, especially in low-resource settings. It has a potential to replace PCR for all purposes, provided its shortcomings are fixed and its reagent accessibility is improved.
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Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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14
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Jiao J, Qi Y, He P, Wan W, OuYang X, Yu Y, Wen B, Xiong X. Development of a Lateral Flow Strip-Based Recombinase-Aided Amplification for Active Chlamydia psittaci Infection. Front Microbiol 2022; 13:928025. [PMID: 35770169 PMCID: PMC9234530 DOI: 10.3389/fmicb.2022.928025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Chlamydia psittaci is the causative agent of psittacosis, a worldwide zoonotic disease. A rapid, specific, and sensitive diagnostic assay would be benefit for C. psittaci infection control. In this study, an assay combining recombinase-aided amplification and a lateral flow strip (RAA-LF) for the detection of active C. psittaci infection was developed. The RAA-LF assay targeted the CPSIT_RS02830 gene of C. psittaci and could be accomplished in 15 min at a single temperature (39°C). The analytical sensitivity of the assay was as low as 1 × 100 copies/μl and no cross-reaction with some other intracellular pathogens was observed. Moreover, all feces samples from mice infected with C. psittaci at day-1 post-infection were positive in the RAA-LF assay. In conclusion, the RAA-LF assay provides a convenient, rapid, specific and sensitive method for detection of active C. psittaci infection and it is also suitable for C. psittaci detection in field.
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Affiliation(s)
- Jun Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yong Qi
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Peisheng He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Weiqiang Wan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xuan OuYang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yonghui Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bohai Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaolu Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *Correspondence: Xiaolu Xiong,
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15
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Wu X, Liu Y, Gao L, Yan Z, Zhao Q, Chen F, Xie Q, Zhang X. Development and Application of a Reverse-Transcription Recombinase-Aided Amplification Assay for Porcine Epidemic Diarrhea Virus. Viruses 2022; 14:v14030591. [PMID: 35336998 PMCID: PMC8948910 DOI: 10.3390/v14030591] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/25/2022] [Accepted: 03/08/2022] [Indexed: 12/29/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a coronavirus currently widespread worldwide in the swine industry. Since PEDV was discovered in China in 1984, it has caused huge economic losses in the swine industry. PEDV can infect pigs of all ages, but piglets have the highest infection with a death rate as high as 100%, and the clinical symptoms are watery diarrhea, vomiting, and dehydration. At present, there is not any report on PEDV detection by RT-RAA. In this study, we developed an isothermal amplification technology by using reverse-transcription recombinase-aided amplification assay (RT-RAA) combined with portable instruments to achieve a molecular diagnosis of PEDV in clinical samples from China. By designing a pair of RT-RAA primers and probes based on the PEDV N gene, this method breaks the limitations of existing detection methods. The assay time was within 30 min at 41 °C and can detect as few as 10 copies of PEDV DNA molecules per reaction. Sixty-two clinical tissue samples were detected by RT-qPCR and RT-RAA. The positive and negative rates for the two methods were 24.19% and 75.81%, respectively. Specificity assay showed that the RT-RAA had specifically detected PEDV and was not reactive for porcine parvovirus (PPV), transmissible gastroenteritis virus (TGEV), porcine circovirus type 2 (PCV2), porcine pseudorabies virus (PRV), porcine reproductive and respiratory syndrome virus (PRRSV), classical swine fever virus (CSFV), swine flu virus (SIV), or porcine Japanese encephalitis virus (JEV). The results suggested that RT-RAA had a strong specificity and high detection sensitivity when combined with a portable instrument to complete the detection under a constant temperature of 30 min, which are more suitable for preventing and controlling PEDV onsite in China.
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Affiliation(s)
- Xiuhong Wu
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.W.); (L.G.); (Q.Z.); (F.C.)
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China
| | - Yuanjia Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
| | - Liguo Gao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.W.); (L.G.); (Q.Z.); (F.C.)
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China
| | - Zhuanqiang Yan
- Guangdong Enterprise Key Laboratory for Animal Health and Environmental Control, Wen’s Foodstuff Group Co., Ltd., Yunfu 527439, China;
| | - Qiqi Zhao
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.W.); (L.G.); (Q.Z.); (F.C.)
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China
| | - Feng Chen
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.W.); (L.G.); (Q.Z.); (F.C.)
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China
| | - Qingmei Xie
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.W.); (L.G.); (Q.Z.); (F.C.)
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China
- Correspondence: (Q.X.); (X.Z.); Tel.: +86-20-8528-0283 (X.Z.); Fax: +86-20-8528-0740 (X.Z.)
| | - Xinheng Zhang
- Heyuan Branch, Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.W.); (L.G.); (Q.Z.); (F.C.)
- Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou 510642, China
- South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou 510642, China
- Correspondence: (Q.X.); (X.Z.); Tel.: +86-20-8528-0283 (X.Z.); Fax: +86-20-8528-0740 (X.Z.)
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16
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Mu D, Zhou D, Xie G, Liu J, Wang Z, Xiong Q, Xu H. Real-time recombinase-aided amplification with PMAxx for the rapid detection of viable Escherichia coli O157:H7 in milk. J Dairy Sci 2022; 105:1028-1038. [PMID: 34998542 DOI: 10.3168/jds.2021-21074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022]
Abstract
Escherichia coli O157:H7, the causative agent of thrombotic thrombocytopenic purpura and hemolytic uremic syndrome in humans, generates a effective harm to community health because of its high pathogenicity. A real-time recombinase-aided amplification (rRAA) is an emerging method for nucleic acid detection. However, genomic DNA of bacteria could exist in food and the environment for a long time after death and could be amplified by rRAA assay, resulting in false-positive signal; thus, developing a fast and sensitive method is necessary to detect viable foodborne pathogens in food products. In our research, rRAA assay coupled with an enhanced nucleic acid binding dye named improved propidium monoazide (PMAxx) was established and applied in viable E. coli O157:H7 identification in skim milk. The PMAxx could eliminate interference from dead bacteria by permeating impaired membranes and covalently linking to DNA to prevent DNA amplification. The PMAxx-rRAA assay was performed with high sensitivity and good specificity. The PMAxx-rRAA assay could detect as low as 5.4 × 100 cfu/mL of viable E. coli O157:H7 in pure culture, and 7.9 × 100 cfu/mL of viable E. coli O157:H7 in skim milk. In addition, the PMAxx-rRAA assay was performed in the presence of a high concentration of dead bacteria or nontarget bacteria in skim milk to verify the capacity to resist interference from dead bacteria and nontarget bacteria. Therefore, the established PMAxx-rRAA assay is a valuable tool for the identification of viable E. coli O157:H7 in complex food matrix.
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Affiliation(s)
- Dan Mu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Donggen Zhou
- Ningbo International Travel Healthcare Center (Ningbo Customs Port Outpatient Department), Ningbo, 315010, PR China
| | - Guoyang Xie
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Ju Liu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Zhengzheng Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Qin Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China.
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17
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Zhang W, Feng Y, Zhao H, Yan C, Feng J, Gan L, Cui J, Liu S, Zhang R, Du S, Li N, Xu W, Han J, Li R, Xue G, Yuan J. A Recombinase Aided Amplification Assay for Rapid Detection of the Klebsiella pneumoniae Carbapenemase Gene and Its Characteristics in Klebsiella pneumoniae. Front Cell Infect Microbiol 2021; 11:746325. [PMID: 34616692 PMCID: PMC8488121 DOI: 10.3389/fcimb.2021.746325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/24/2021] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase genes (blaKPC) play an important role in carbapenem-resistant Enterobacteriaceae in China. A rapid detection method for blaKPC genes and investigations into the molecular characteristics of blaKPC positive Klebsiella pneumoniae were necessary. In this study, an easy and rapid recombinase aided amplification assay (RAA) for blaKPC was established. This protocol could be completed at 39°C in 15–20 min. The sensitivity of this assay was determined as 48 copies per reaction, and the specificity was 100%. The blaKPC RAA method could be used for clinical diagnosis and epidemiological investigation. Among 801 fecal samples from inpatients, 34 blaKPC positive isolates were identified from each sample, of which 23 isolates were K. pneumoniae. ST11 with blaKPC-2 was the most prevalent type. All these strains were multidrug resistant and carried various virulence genes. Fecal carriage of blaKPC positive carbapenem-resistant K.pneumoniae poses significant challenges for public health control.
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Affiliation(s)
- Weiwei Zhang
- The Second Affiliated Hospital of Dalian Medical University, Liaoning, China.,Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shiyu Liu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Nannan Li
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Wenjian Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Juqiang Han
- Department of Daily Clinic, Seventh Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Rongkuan Li
- The Second Affiliated Hospital of Dalian Medical University, Liaoning, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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