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Arevalo-Rodriguez I, Mateos-Haro M, Dinnes J, Ciapponi A, Davenport C, Buitrago-Garcia D, Bennouna-Dalero T, Roqué-Figuls M, Van den Bruel A, von Eije KJ, Emperador D, Hooft L, Spijker R, Leeflang MM, Takwoingi Y, Deeks JJ. Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2024; 10:CD015618. [PMID: 39400904 DOI: 10.1002/14651858.cd015618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
BACKGROUND Diagnosing people with a SARS-CoV-2 infection played a critical role in managing the COVID-19 pandemic and remains a priority for the transition to long-term management of COVID-19. Initial shortages of extraction and reverse transcription polymerase chain reaction (RT-PCR) reagents impaired the desired upscaling of testing in many countries, which led to the search for alternatives to RNA extraction/purification and RT-PCR testing. Reference standard methods for diagnosing the presence of SARS-CoV-2 infection rely primarily on real-time reverse transcription-polymerase chain reaction (RT-PCR). Alternatives to RT-PCR could, if sufficiently accurate, have a positive impact by expanding the range of diagnostic tools available for the timely identification of people infected by SARS-CoV-2, access to testing and the use of resources. OBJECTIVES To assess the diagnostic accuracy of alternative (to RT-PCR assays) laboratory-based molecular tests for diagnosing SARS-CoV-2 infection. SEARCH METHODS We searched the COVID-19 Open Access Project living evidence database from the University of Bern until 30 September 2020 and the WHO COVID-19 Research Database until 31 October 2022. We did not apply language restrictions. SELECTION CRITERIA We included studies of people with suspected or known SARS-CoV-2 infection, or where tests were used to screen for infection, and studies evaluating commercially developed laboratory-based molecular tests for the diagnosis of SARS-CoV-2 infection considered as alternatives to RT-PCR testing. We also included all reference standards to define the presence or absence of SARS-CoV-2, including RT-PCR tests and established clinical diagnostic criteria. DATA COLLECTION AND ANALYSIS Two authors independently screened studies and resolved disagreements by discussing them with a third author. Two authors independently extracted data and assessed the risk of bias and applicability of the studies using the QUADAS-2 tool. We presented sensitivity and specificity, with 95% confidence intervals (CIs), for each test using paired forest plots and summarised results using average sensitivity and specificity using a bivariate random-effects meta-analysis. We illustrated the findings per index test category and assay brand compared to the WHO's acceptable sensitivity and specificity threshold for diagnosing SARS-CoV-2 infection using nucleic acid tests. MAIN RESULTS We included data from 64 studies reporting 94 cohorts of participants and 105 index test evaluations, with 74,753 samples and 7517 confirmed SARS-CoV-2 cases. We did not identify any published or preprint reports of accuracy for a considerable number of commercially produced NAAT assays. Most cohorts were judged at unclear or high risk of bias in more than three QUADAS-2 domains. Around half of the cohorts were considered at high risk of selection bias because of recruitment based on COVID status. Three quarters of 94 cohorts were at high risk of bias in the reference standard domain because of reliance on a single RT-PCR result to determine the absence of SARS-CoV-2 infection or were at unclear risk of bias due to a lack of clarity about the time interval between the index test assessment and the reference standard, the number of missing results, or the absence of a participant flow diagram. For index tests categories with four or more evaluations and when summary estimations were possible, we found that: a) For RT-PCR assays designed to omit/adapt RNA extraction/purification, the average sensitivity was 95.1% (95% CI 91.1% to 97.3%), and the average specificity was 99.7% (95% CI 98.5% to 99.9%; based on 27 evaluations, 2834 samples and 1178 SARS-CoV-2 cases); b) For RT-LAMP assays, the average sensitivity was 88.4% (95% CI 83.1% to 92.2%), and the average specificity was 99.7% (95% CI 98.7% to 99.9%; 24 evaluations, 29,496 samples and 2255 SARS-CoV-2 cases); c) for TMA assays, the average sensitivity was 97.6% (95% CI 95.2% to 98.8%), and the average specificity was 99.4% (95% CI 94.9% to 99.9%; 14 evaluations, 2196 samples and 942 SARS-CoV-2 cases); d) for digital PCR assays, the average sensitivity was 98.5% (95% CI 95.2% to 99.5%), and the average specificity was 91.4% (95% CI 60.4% to 98.7%; five evaluations, 703 samples and 354 SARS-CoV-2 cases); e) for RT-LAMP assays omitting/adapting RNA extraction, the average sensitivity was 73.1% (95% CI 58.4% to 84%), and the average specificity was 100% (95% CI 98% to 100%; 24 evaluations, 14,342 samples and 1502 SARS-CoV-2 cases). Only two index test categories fulfil the WHO-acceptable sensitivity and specificity requirements for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. In addition, WHO-acceptable performance criteria were met for two assays out of 35 when tests were used according to manufacturer instructions. At 5% prevalence using a cohort of 1000 people suspected of SARS-CoV-2 infection, the positive predictive value of RT-PCR assays omitting/adapting RNA extraction/purification will be 94%, with three in 51 positive results being false positives, and around two missed cases. For TMA assays, the positive predictive value of RT-PCR assays will be 89%, with 6 in 55 positive results being false positives, and around one missed case. AUTHORS' CONCLUSIONS Alternative laboratory-based molecular tests aim to enhance testing capacity in different ways, such as reducing the time, steps and resources needed to obtain valid results. Several index test technologies with these potential advantages have not been evaluated or have been assessed by only a few studies of limited methodological quality, so the performance of these kits was undetermined. Only two index test categories with enough evaluations for meta-analysis fulfil the WHO set of acceptable accuracy standards for SARS-CoV-2 nucleic acid tests: RT-PCR assays designed to omit/adapt RNA extraction/purification and TMA assays. These assays might prove to be suitable alternatives to RT-PCR for identifying people infected by SARS-CoV-2, especially when the alternative would be not having access to testing. However, these findings need to be interpreted and used with caution because of several limitations in the evidence, including reliance on retrospective samples without information about the symptom status of participants and the timing of assessment. No extrapolation of found accuracy data for these two alternatives to any test brands using the same techniques can be made as, for both groups, one test brand with high accuracy was overrepresented with 21/26 and 12/14 included studies, respectively. Although we used a comprehensive search and had broad eligibility criteria to include a wide range of tests that could be alternatives to RT-PCR methods, further research is needed to assess the performance of alternative COVID-19 tests and their role in pandemic management.
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Affiliation(s)
- Ingrid Arevalo-Rodriguez
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS). CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Evidence Production & Methods Directorate, Cochrane, London, UK
| | - Miriam Mateos-Haro
- Clinical Biostatistics Unit, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- Doctoral programme in Clinical Medicine and Public Health, Universidad de Granada, Granada, Spain
| | - Jacqueline Dinnes
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Agustín Ciapponi
- Argentine Cochrane Centre, Institute for Clinical Effectiveness and Health Policy (IECS-CONICET), Buenos Aires, Argentina
| | - Clare Davenport
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Diana Buitrago-Garcia
- Institute for Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Hospital Universitario Mayor - Méderi. Universidad del Rosario, Bogotá, Colombia
| | - Tayeb Bennouna-Dalero
- Preventive Medicine and Public Health Department, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Marta Roqué-Figuls
- Iberoamerican Cochrane Centre, Institut de Recerca Sant Pau (IR SANT PAU), CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | | | - Karin J von Eije
- Department of Viroscience, ErasmusMC, University Medical Center, Rotterdam, Netherlands
| | | | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - René Spijker
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Yemisi Takwoingi
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- Department of Applied Health Sciences, School of Health Sciences, College of Medicine and Health, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
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Kachwala MJ, Hamdard F, Cicek D, Dagci H, Smith CW, Kalla N, Yigit MV. Universal CRISPR-Cas12a and Toehold RNA Cascade Reaction on Paper Substrate for Visual Salmonella Genome Detection. Adv Healthc Mater 2024; 13:e2400508. [PMID: 38683016 DOI: 10.1002/adhm.202400508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/12/2024] [Indexed: 05/01/2024]
Abstract
Salmonella, the most prevalent food-borne pathogen, poses significant medical and economic threats. Swift and accurate on-site identification and serotyping of Salmonella is crucial to curb its spread and contamination. Here, a synthetic biology cascade reaction is presented on a paper substrate using CRISPR-Cas12a and recombinase polymerase amplification (RPA), enabling the programming of a standard toehold RNA switch for a genome of choice. This approach employs just one toehold RNA switch design to differentiate between two different Salmonella serotypes, i.e., S. Typhimurium and S. Enteritidis, without the need for reengineering the toehold RNA switch. The sensor exhibits high sensitivity, capable of visually detecting as few as 100 copies of the whole genome from a model Salmonella pathogen on a paper substrate. Furthermore, this robust assay is successfully applied to detect whole genomes in contaminated milk and lettuce samples, demonstrating its potential in real sample analysis. Due to its versatility and practical features, genomes from different organisms can be detected by merely changing a single RNA element in this universal cell-free cascade reaction.
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Affiliation(s)
- Mahera J Kachwala
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Farishta Hamdard
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Damla Cicek
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Hilal Dagci
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Nabeel Kalla
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
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Zhang X, Wu X, Feng K, Wang Q, Xie Q. A New Dual Fluorescence Method for Rapid Detection of Infectious Bronchitis Virus at Constant Temperature. Microorganisms 2024; 12:1315. [PMID: 39065085 PMCID: PMC11279307 DOI: 10.3390/microorganisms12071315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024] Open
Abstract
Infectious bronchitis virus (IBV) causes infectious bronchitis in chicken, an acute, highly contagious respiratory infection. Because of genetic mutations and recombination, IBV forms many subtypes, which makes it difficult to treat the disease and apply commercial vaccines. Therefore, to detect IBV in time and stop the virus from spreading, a novel and convenient IBV detection technology based on reverse transcription recombinase-aided amplification (RT-RAA) was established in this study. According to the S1 gene of IBV CH I-V and Mass genotypes and S1 gene of IBV CH VI genotype, a set of optimal primers were designed and selected to establish a real-time dual fluorescence RT-RAA method. The lowest detection line was 10 copies/μL of RNA molecules and the method exhibited no cross-reactivity with avian reticuloendotheliosis virus (REV), infectious bursal disease virus (IBDV), avian leukosis virus (ALV), Newcastle disease virus (NDV), chicken infectious anemia virus (CIAV), infectious laryngotracheitis virus (ILTV), Marek's disease virus (MDV), and H9N2 avian influenza virus (H9N2), demonstrating high specificity. When compared to qPCR detection results, our method achieved a sensitivity of 96.67%, a specificity of 90%, and a Kappa value of 0.87 for the IBV CH I-V and Mass genotypes, and achieved a sensitivity of 100%, a specificity of 97.73%, and a Kappa value of 0.91 for the IBV CH VI genotype.
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Affiliation(s)
- Xinheng Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (X.W.); (K.F.); (Q.W.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517000, China
- 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
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiuhong Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (X.W.); (K.F.); (Q.W.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517000, China
- 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
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Keyu Feng
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (X.W.); (K.F.); (Q.W.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517000, China
- 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
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qian Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (X.W.); (K.F.); (Q.W.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517000, China
- 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
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qingmei Xie
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou 510642, China; (X.Z.); (X.W.); (K.F.); (Q.W.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517000, China
- 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
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou 510642, China
- Guangdong Provincial Key Lab of AgroAnimal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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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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Heng P, Shi B, Li D, Ou H, He Y, Zhou L. Rapid visualization molecular fluorescence detection of methicillin-resistant Staphylococcus aureus using the multiplex MIRA-qPCR method. Biotechnol J 2023; 18:e2300200. [PMID: 37626194 DOI: 10.1002/biot.202300200] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023]
Abstract
Multidrug-resistant (MDR) bacterial infections constitute a major public health problem worldwide. A rapid method for the detection of methicillin-resistant Staphylococcus aureus (MRSA) is critical for the timely prevention of bacterial infections and the accurate clinical use of drugs. The nuc and mecA genes are potentially indicative of MRSA infection and in this study, a multiplex molecular fluorescence multi-enzyme isothermal rapid amplification visual assay was proposed and established. The method is capable of detecting MRSA at 17 min, 40°C amplification, and is well differentiated from common clinical bacteria in specific assays, with 500 colony-forming units (CFU) mL-1 of MRSA detected under optimal conditions. This method has excellent diagnostic capabilities versus classical methods to detect clinical samples and shows potential in the identification of pathogenic microorganisms in a clinical setting.
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Affiliation(s)
- Pengfei Heng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Bo Shi
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan, China
| | - Dongmei Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Hua Ou
- Department of Laboratory Medicine, People's Hospital of Xinjin District, Chengdu, Sichuan, China
| | - Yang He
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Lili Zhou
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, Sichuan, China
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Homklinkaew P, Phatthanakunanan S, Jala S, Boonsoongnern A, Lertwatcharasarakul P. Development of a recombinase-aided amplification method combined with lateral flow dipstick assay to detect Porcine circovirus type 2. Vet World 2023; 16:2313-2320. [PMID: 38152256 PMCID: PMC10750741 DOI: 10.14202/vetworld.2023.2313-2320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/16/2023] [Indexed: 12/29/2023] Open
Abstract
Background and Aim Porcine circovirus type 2 (PCV2) is a pathogenic virus that suppresses the immune system of pigs, impacting their health and causing economic losses. Rapid diagnostic tools for early detection of PCV2 are critical to disease prevention and control. Several molecular techniques have been established for detecting PCV2 but costly equipment and time-consuming methods are unsuitable for field inspection. In this study, we developed a recombinase-aided amplification combined with lateral flow dipstick (RAA-LFD) assay to compare with polymerase chain reaction (PCR) and quantitative PCR (qPCR) in detecting PCV2 in suspected field samples. Materials and Methods To amplify RAA products, 15 primer pairs were designed from the conserved region of the open reading frame (ORF) 1 gene based on multiple alignments of eight PCV2 genotypes. The most efficient primer pair and conditions for the RAA-LFD assay were tested and selected. Limit of detection, repeatability, and reproducibility were determined using the constructed plasmid. DNA was extracted from positive samples for specificity testing as well as from 100 field samples to compare the detection of the RAA-LFD assay with PCR and qPCR. Results The F1/R1 primer pair was chosen and labeled with fluorescein isothiocyanate at the 5' end of the forward primer and with biotin at the 5' end of the reverse primer. The limit of detection of the RAA-LFD assay was 10 copies/μL at 38°C for 30 min. The RAA-LFD assay was repeatable and reproducible, with no cross-reaction with PCV3, Actinobacillus pleuropneumoniae, Porcine epidemic diarrhea virus, Classical swine fever virus, Porcine reproductive and respiratory syndrome virus - North America strain (PRRSV-US) and Porcine reproductive and respiratory syndrome virus - European strain (PRRSV-EU). Based on testing with 100 samples, the developed RAA showed 100% specificity and 90.56% and 85.71% sensitivity when compared to PCR and qPCR, respectively Cohen's kappa coefficients showed a good agreement with the established techniques. Conclusion The RAA-LFD assay targeting the ORF1 gene was highly sensitive, specific, quick, and simple to perform in the field.
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Affiliation(s)
- Ploypassorn Homklinkaew
- Animal Health and Biomedical Sciences Study Program, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Sakuna Phatthanakunanan
- Kamphaeng Saen Veterinary Diagnostic Center, Faculty of Veterinary Medicine, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Siriluk Jala
- Kamphaeng Saen Veterinary Diagnostic Center, Faculty of Veterinary Medicine, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Alongkot Boonsoongnern
- Department of Farm Resources and Production Medicine, Faculty of Veterinary Medicine, Kasetsart University, Nakorn Pathom 73140, Thailand
| | - Preeda Lertwatcharasarakul
- Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Nakorn Pathom 73140, Thailand
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Reynolds J, Loeffler RS, Leigh PJ, Lopez HA, Yoon JY. Recent Uses of Paper Microfluidics in Isothermal Nucleic Acid Amplification Tests. BIOSENSORS 2023; 13:885. [PMID: 37754119 PMCID: PMC10526735 DOI: 10.3390/bios13090885] [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: 08/15/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023]
Abstract
Isothermal nucleic acid amplification tests have recently gained popularity over polymerase chain reaction (PCR), as they only require a constant temperature and significantly simplify nucleic acid amplification. Recently, numerous attempts have been made to incorporate paper microfluidics into these isothermal amplification tests. Paper microfluidics (including lateral flow strips) have been used to extract nucleic acids, amplify the target gene, and detect amplified products, all toward automating the process. We investigated the literature from 2020 to the present, i.e., since the onset of the COVID-19 pandemic, during which a significant surge in isothermal amplification tests has been observed. Paper microfluidic detection has been used extensively for recombinase polymerase amplification (RPA) and its related methods, along with loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA). Detection was conducted primarily with colorimetric and fluorometric methods, although a few publications demonstrated flow distance- and surface-enhanced Raman spectroscopic (SERS)-based detection. A good number of publications could be found that demonstrated both amplification and detection on paper microfluidic platforms. A small number of publications could be found that showed extraction or all three procedures (i.e., fully integrated systems) on paper microfluidic platforms, necessitating the need for future work.
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Affiliation(s)
- Jocelyn Reynolds
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Reid S. Loeffler
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Preston J. Leigh
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
| | - Hannah A. Lopez
- Department of Neuroscience, The University of Arizona, Tucson, AZ 85721, USA;
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA; (J.R.); (R.S.L.); (P.J.L.)
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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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Li X, Zhu S, Zhang X, Ren Y, He J, Zhou J, Yin L, Wang G, Zhong T, Wang L, Xiao Y, Zhu C, Yin C, Yu X. Advances in the application of recombinase-aided amplification combined with CRISPR-Cas technology in quick detection of pathogenic microbes. Front Bioeng Biotechnol 2023; 11:1215466. [PMID: 37720320 PMCID: PMC10502170 DOI: 10.3389/fbioe.2023.1215466] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
The rapid diagnosis of pathogenic infections plays a vital role in disease prevention, control, and public health safety. Recombinase-aided amplification (RAA) is an innovative isothermal nucleic acid amplification technology capable of fast DNA or RNA amplification at low temperatures. RAA offers advantages such as simplicity, speed, precision, energy efficiency, and convenient operation. This technology relies on four essential components: recombinase, single-stranded DNA-binding protein (SSB), DNA polymerase, and deoxyribonucleoside triphosphates, which collectively replace the laborious thermal cycling process of traditional polymerase chain reaction (PCR). In recent years, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) system, a groundbreaking genome engineering tool, has garnered widespread attention across biotechnology, agriculture, and medicine. Increasingly, researchers have integrated the recombinase polymerase amplification system (or RAA system) with CRISPR technology, enabling more convenient and intuitive determination of detection results. This integration has significantly expanded the application of RAA in pathogen detection. The step-by-step operation of these two systems has been successfully employed for molecular diagnosis of pathogenic microbes, while the single-tube one-step method holds promise for efficient pathogen detection. This paper provides a comprehensive review of RAA combined with CRISPR-Cas and its applications in pathogen detection, aiming to serve as a valuable reference for further research in related fields.
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Affiliation(s)
- Xiaoping Li
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Shuying Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Xinling Zhang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Yanli Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, 310003, China
| | - Jing He
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Jiawei Zhou
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Liliang Yin
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Gang Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang Province, 310015, China
| | - Tian Zhong
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Ling Wang
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Ying Xiao
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Guangdong-Hong Kong-Macau Joint Laboratory for Contaminants Exposure and Health, Guangzhou, Guangdong Province, 510006, China
| | - Chunying Zhu
- Clinical Psychology Department, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, Zhejiang Province, 310005, China
| | - Chengliang Yin
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
| | - Xi Yu
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, 999078, China
- Guangdong-Hong Kong-Macau Joint Laboratory for Contaminants Exposure and Health, Guangzhou, Guangdong Province, 510006, China
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Wang F, Liang Q, Lv R, Ahmad S, Bano M, Weng G, Wen R. Optimization and Validation of Reverse Transcription Recombinase-Aided Amplification (RT-RAA) for Sorghum Mosaic Virus Detection in Sugarcane. Pathogens 2023; 12:1055. [PMID: 37624015 PMCID: PMC10457762 DOI: 10.3390/pathogens12081055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Sorghum mosaic virus (SrMV) causes sugarcane mosaic disease and has significant adverse economic impacts on the cultivation of sugarcane. This study aimed to develop a rapid isotherm nucleic acid amplification method for detecting SrMV. Specific primers were designed to target the conserved region of the P3 gene of SrMV. The reverse transcription recombinase-aided amplification (RT-RAA) method was developed by screening primers and optimizing reaction conditions. Comparative analyses with RT-PCR demonstrated that the RT-RAA method exhibited superior specificity, sensitivity, and reliability for SrMV detection. Notably, using a standard plasmid diluted 10-fold continuously as a template, the sensitivity of RT-RAA was 100-fold higher than that of RT-PCR. Moreover, the RT-RAA reaction displayed flexibility in a temperature range of 24-49 °C, eliminating the need for expensive and complex temperature control equipment. Thus, this method could be utilized at ambient or even human body temperature. Within a short duration of 10 min at 39 °C, the target sequence of SrMV could be effectively amplified. Specificity analysis revealed no cross-reactivity between SrMV and other common sugarcane viruses detected via the RT-RAA. With its high sensitivity, rapid reaction time, and minimal equipment requirements, this method presents a promising diagnostic tool for the reliable and expedited detection of SrMV. Furthermore, it indicates broad applicability for successfully detecting other sugarcane viruses.
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Affiliation(s)
| | | | | | | | | | | | - Ronghui Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Ministry and Province Co-Sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China; (F.W.); (Q.L.); (R.L.); (S.A.); (M.B.); (G.W.)
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11
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Ding X, Yang Y, Zhang Y, Zhang Q, Mao F, Dai Y. Establishment of a Simple and Rapid Nucleic Acid Detection Method for Hookworm Identification. Pathogens 2023; 12:pathogens12040630. [PMID: 37111516 PMCID: PMC10142964 DOI: 10.3390/pathogens12040630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Hookworm infection is one of the most common neglected tropical diseases and is mainly found in tropical and subtropical areas. Two species of human hookworm are distributed in China, i.e., Ancylostoma duodenale (AD) and Necator americanus (NA). BACKGROUND Traditional microscopic technology such as the Kato-Katz method is not suitable for hookworm diagnosis due to the rapid degeneration of fragile hookworm eggs or for species identification of hookworm infection. The aim of the present study was to establish and evaluate a novel nucleic acid detection method based on recombinase-aided isothermal amplification (RAA) for the detection of hookworm infections and species identification. METHODS Based on the specific target gene sequences of hookworms (5.8S rRNA for AD and ITS2 for NA, respectively), we designed and synthesized amplification primers and fluorescence probes referring to the principle of the fluorescence recombinase-aided amplification (RAA) technique. RESULTS Each assay provided specific amplification of larval DNA from AD and NA by fluorescence RAA, and the detection limits in plasmids reached 102 copies and 10 copies, respectively. Genomic DNA of two hookworm species was successfully detected at a concentration of 0.1 pg/μL, revealing a high detection sensitivity. No positive amplification occurred for genomic DNA from crossed hookworm species and genomic DNA from Cryptosporidium, Giardia lamblia, Strongyloides stercoralis, Schistosoma japonicum, Ascaris lumbricoides, and Clonorchis sinensis, revealing a satisfactory specificity. Fecal sample detection results demonstrated a similar efficacy to the Kato-Katz method; however, it had a greater sensitivity than the larvae culture method. CONCLUSION A simple and rapid nucleic acid method was successfully established based on RAA, which improved the detection efficacy and species identification for human hookworm infections.
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Affiliation(s)
- Xin Ding
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Key Laboratory of Jiangsu Province on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Yougui Yang
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yingshu Zhang
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qiang Zhang
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Key Laboratory of Jiangsu Province on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Fanzhen Mao
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Key Laboratory of Jiangsu Province on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Yang Dai
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Key Laboratory of Jiangsu Province on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
- School of Public Health, Nanjing Medical University, Nanjing 211166, China
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12
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Wu S, Yuan J, Xu A, Wang L, Li Y, Lin J, Yue X, Xi X. A Lab-on-a-Tube Biosensor Combining Recombinase-Aided Amplification and CRISPR-Cas12a with Rotated Magnetic Extraction for Salmonella Detection. MICROMACHINES 2023; 14:830. [PMID: 37421063 DOI: 10.3390/mi14040830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Foodborne pathogenic bacteria threaten worldwide public health, and simple bacterial detection methods are in urgent need. Here, we established a lab-on-a-tube biosensor for simple, rapid, sensitive, and specific detection of foodborne bacteria. METHODS A rotatable Halbach cylinder magnet and an iron wire netting with magnetic silica beads (MSBs) were used for simple and effective extraction and purification of DNA from the target bacteria, and recombinase-aided amplification (RAA) was combined with clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins12a(CRISPR-Cas12a) to amplify DNA and generate fluorescent signal. First, 15 mL of the bacterial sample was centrifuged, and the bacterial pellet was lysed by protease to release target DNA. Then, DNA-MSB complexes were formed as the tube was intermittently rotated and distributed uniformly onto the iron wire netting inside the Halbach cylinder magnet. Finally, the purified DNA was amplified using RAA and quantitatively detected by the CRISPR-Cas12a assay. RESULTS This biosensor could quantitatively detect Salmonella in spiked milk samples in 75 min, with a lower detection limit of 6 CFU/mL. The fluorescent signal of 102 CFU/mL Salmonella Typhimurium was over 2000 RFU, while 104 CFU/mL Listeria monocytogenes, Bacillus cereus, and E. coli O157:H7 were selected as non-target bacteria and had signals less than 500 RFU (same as the negative control). CONCLUSIONS This lab-on-a-tube biosensor integrates cell lysis, DNA extraction, and RAA amplification in one 15 mL tube to simplify the operation and avoid contamination, making it suitable for low-concentration Salmonella detection.
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Affiliation(s)
- Shangyi Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Jing Yuan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Ai Xu
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Lei Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinge Xi
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
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13
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Paramithiotis S. Molecular Targets for Foodborne Pathogenic Bacteria Detection. Pathogens 2023; 12:pathogens12010104. [PMID: 36678453 PMCID: PMC9865778 DOI: 10.3390/pathogens12010104] [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: 11/30/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The detection of foodborne pathogenic bacteria currently relies on their ability to grow on chemically defined liquid and solid media, which is the essence of the classical microbiological approach. Such procedures are time-consuming and the quality of the result is affected by the selectivity of the media employed. Several alternative strategies based on the detection of molecular markers have been proposed. These markers may be cell constituents, may reside on the cell envelope or may be specific metabolites. Each marker provides specific advantages and, at the same time, suffers from specific limitations. The food matrix and chemical composition, as well as the accompanying microbiota, may also severely compromise detection. The aim of the present review article is to present and critically discuss all available information regarding the molecular targets that have been employed as markers for the detection of foodborne pathogens. Their strengths and limitations, as well as the proposed alleviation strategies, are presented, with particular emphasis on their applicability in real food systems and the challenges that are yet to be effectively addressed.
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Affiliation(s)
- Spiros Paramithiotis
- Laboratory of Food Process Engineering, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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14
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Zhong Y, Liu M, Ding Y, Wu Q, Zhang J, Ma G, Xu T, Wang Z, Chen M, Xue L, Ye Q, Wang J. Rapid fluorescence visualization of Yersinia enterocolitica by CRISPR/Cas12a using novel specific target obtained by pan-genome analysis. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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15
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Fang T, Shen J, Xue J, Jiang Y, Guo D, Yang J, Kong X, Xu X, Wang X. Sensitive and Rapid Detection of Escherichia coli O157:H7 From Beef Samples Based on Recombinase Aided Amplification Assisted CRISPR/Cas12a System. J AOAC Int 2022; 106:156-164. [PMID: 36005831 DOI: 10.1093/jaoacint/qsac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Escherichia coli O157:H7, being the cause of hemorrhagic colitis in humans, is recognized as one of the most dangerous and widespread foodborne pathogens. A highly specific, sensitive, and rapid E. coli O157:H7 detection method needs to be developed since the traditional detection methods are complex, costly, and time-consuming. OBJECTIVE In this study, a recombinase aided amplification (RAA) assisted CRISPR/Cas12a (RAA-CRISPR/Cas12a) fluorescence platform for specific, sensitive, and rapid nucleic acid detection of E. coli O157:H7 was introduced. METHODS First, the feasibility (components of CRISPR/Cas12a system) of the developed method was evaluated. Then a total of 34 bacterial strains were used for the specificity test, and gradient dilutions of extracted DNA and bacterial solutions of E. coli O157:H7 were prepared for the sensitivity test. Third, a real-time PCR assay for detection of the specific wzy gene of E. coli O157:H7 (FDA's Bacteriological Analytical Manual) was used for sensitivity comparison. Finally, analysis of RAA-CRISPR/Cas12a detection in spiked and 93 real ground beef samples was carried out. RESULTS The developed RAA-CRISPR/Cas12a method showed high specificity, and the detection could be completed within 30 min (after 4 h enrichment in spiked ground beef samples). The limit of detection (LOD) of bacterial concentrations and genomic DNA was 5.4 × 102 CFU/mL and 7.5 × 10-4 ng/μL, respectively, which exhibited higher sensitivity than the RAA-gel electrophoresis and RT-PCR methods. Furthermore, it was shown that E. coli O157:H7 in ground beef samples could be positively detected after 4 h enrichment when the initial bacterial inoculum was 9.0 CFU/25 g. The detection results of the RAA-CRISPR/Cas12a method were 100% consistent with those of the RT-PCR and traditional culture-based methods while screening the E. coli O157:H7 from 93 local collected ground beef samples. CONCLUSIONS The developed RAA-CRISPR/Cas12a method showed high specificity, high sensitivity, and rapid positive detection of E. coli O157:H7 from ground beef samples. HIGHLIGHTS The RAA-CRISPR/Cas12a system proposed in this study provided an alternative molecular tool for quick, specific, sensitive, and accurate detection of E. coli O157:H7 in foods.
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Affiliation(s)
- Taisong Fang
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Jinling Shen
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Junxin Xue
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Yuan Jiang
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Dehua Guo
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Jielin Yang
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Xiangxiang Kong
- Shanghai University, School of Life Sciences, Shanghai 200444, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Xiang Wang
- University of Shanghai for Science and Technology, School of Health Science and Engineering, Shanghai 400715, China
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Development of a Real-Time Recombinase-Aided Amplification Method to Rapidly Detect Methicillin-Resistant Staphylococcus aureus. Microorganisms 2022; 10:microorganisms10122351. [PMID: 36557604 PMCID: PMC9784193 DOI: 10.3390/microorganisms10122351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/03/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2022] Open
Abstract
Methicillin-resistant staphylococcus aureus (MRSA) is a major pathogen responsible for human hospital and community-onset diseases and severe invasive livestock infections. Rapid detection of MRSA is essential to control the spread of MRSA. Conventional identification methods and antibacterial susceptibility tests of MRSA are time-consuming. The commonly used qPCR assay also has the disadvantages of being complicated and expensive, restricting its application in resource-limited clinical laboratories. Here, a real-time fluorescent recombinase-assisted amplification (RAA) assay targeting the most conserved regions within the mecA gene of MRSA was developed and evaluated to detect MRSA. The detection limit of this assay was determined to be 10 copies/reaction of positive plasmids. The established RAA assay showed high specificity for MRSA detection without cross-reactivities with other clinically relevant bacteria. The diagnostic performance of real-time RAA was evaluated using 67 clinical S. aureus isolates from dairy farms, which were detected in parallel using the TaqMan probe qPCR assay. The results showed that 56 and 54 samples tested positive for MRSA by RAA and qPCR, respectively. The overall agreement between both assays was 97.01% (65/67), with a kappa value of 0.9517 (p < 0.001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9012, p < 0.0001), indicating that this RAA assay possesses similar detection performance to the qPCR assay. In conclusion, our newly established RAA assay is a time-saving and convenient diagnostic tool suitable for MRSA detection and screening.
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17
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Liu J, Wu D, Chen J, Jia S, Chen J, Wu Y, Li G. CRISPR-Cas systems mediated biosensing and applications in food safety detection. Crit Rev Food Sci Nutr 2022; 64:2960-2985. [PMID: 36218189 DOI: 10.1080/10408398.2022.2128300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Food safety, closely related to economic development of food industry and public health, has become a global concern and gained increasing attention worldwide. Effective detection technology is of great importance to guarantee food safety. Although several classical detection methods have been developed, they have some limitations in portability, selectivity, and sensitivity. The emerging CRISPR-Cas systems, uniquely integrating target recognition specificity, signal transduction, and efficient signal amplification abilities, possess superior specificity and sensitivity, showing huge potential to address aforementioned challenges and develop next-generation techniques for food safety detection. In this review, we focus on recent progress of CRISPR-Cas mediated biosensing and their applications in food safety monitoring. The properties and principles of commonly used CRISPR-Cas systems are highlighted. Notably, the frequently coupled nucleic acid amplification strategies to enhance their selectivity and sensitivity, especially isothermal amplification methods, as well as various signal output modes are also systematically summarized. Meanwhile, the application of CRISPR-Cas systems-based biosensors in food safety detection including foodborne virus, foodborne bacteria, food fraud, genetically modified organisms (GMOs), toxins, heavy metal ions, antibiotic residues, and pesticide residues is comprehensively described. Furthermore, the current challenges and future prospects in this field are tentatively discussed.
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Affiliation(s)
- Jianghua Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Jiahui Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Shijie Jia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Jian Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
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18
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Wang S, Qi W, Wu S, Yuan J, Duan H, Li Y, Lin J. An automatic centrifugal system for rapid detection of bacteria based on immunomagnetic separation and recombinase aided amplification. LAB ON A CHIP 2022; 22:3780-3789. [PMID: 36073207 DOI: 10.1039/d2lc00650b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study reported an automatic centrifugal system for rapid quantification of foodborne pathogenic bacteria based on immunomagnetic separation (IMS) for target bacteria enrichment and recombinase aided amplification (RAA) for nucleic acid detection. First, target bacteria were captured by immune magnetic nanoparticles (MNPs) to form magnetic bacteria, which were purified and enriched by magnetic separation. Then, nucleic acid extraction buffer was used to extract genomic DNA of magnetic bacteria and dissolve lyophilized RAA reagent. Finally, isothermal amplification and fluorescent detection were conducted for bacteria quantification. Bacteria magnetic separation, nucleic acid extraction and fluorescent RAA detection were elaborately achieved in a centrifugal disc with unique functional chambers and multistage siphon channels. A supporting device was developed to automatically and successively perform the programmed centrifugal protocol, including temperature control for isothermal amplification and fluorescence detection for real-time RAA analysis. Under optimal conditions, this centrifugal system enabled Salmonella detection as low as 10 CFU mL-1 in spiked chicken samples in 1 h with average recovery of 105.6% and average standard deviation of 8.4%. It has been demonstrated as an alternative for rapid detection of Salmonella.
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Affiliation(s)
- Siyuan Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China.
- Key Laboratory of Smart Agriculture System Integration, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Wuzhen Qi
- Beijing University of Chinese Medicine, School of Chinese Materia Medica, Beijing 100029, China
| | - Shangyi Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Jing Yuan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China.
| | - Hong Duan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China.
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China.
- Key Laboratory of Smart Agriculture System Integration, Ministry of Education, China Agricultural University, Beijing 100083, China
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19
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Cheng P, Wu Y, Guo S, Ma X, Fei C, Xue F, Zhu C, Wang M, Gu F. RPA assay coupled with CRISPR/Cas12a system for the detection of seven Eimeria species in chicken fecal samples. Vet Parasitol 2022; 311:109810. [PMID: 36183557 DOI: 10.1016/j.vetpar.2022.109810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/18/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022]
Abstract
Chicken coccidiosis is one of the most common and economically important diseases in the global poultry industry, and it is caused by at least one of the seven Eimeria species. A simple and reliable way to distinguish Eimeria species in infected chicken is critical for the surveillance, control, and eradication of chicken coccidiosis. In this study, a recombinase polymerase amplification (RPA) assay coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system (RPA-CRISPR/Cas12a) was developed for the detection of Eimeria species in chicken fecal samples. This assay is highly specific to the seven Eimeria species and it does not cross react between species. Assessment of analytical sensitivity revealed that a single copy of plasmid DNA could be detected. Comparative analysis revealed strong agreement between RPA-CRISPR/Cas12a assays and real-time qPCR to reliably detect all seven Eimeria species in fecal chicken samples. Importantly, the cleavage products could be visualized under a blue light instrument, making it possible for the rapid detection of Eimeria species for on-site testing. Collectively, our study demonstrated that RPA-CRISPR/Cas12a assays offer a simple and reliable diagnostic method for Eimeria species.
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Affiliation(s)
- Peipei Cheng
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Yuting Wu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Shuangshuang Guo
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Xiaoyu Ma
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Chenzhong Fei
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Feiqun Xue
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Chuangang Zhu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Mi Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Feng Gu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
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20
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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: 6] [Impact Index Per Article: 3.0] [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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21
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Wu S, Duan H, Zhang Y, Wang S, Zheng L, Cai G, Lin J, Yue X. A Salmonella Microfluidic Chip Combining Non-Contact Eddy Heater and 3D Fan-Shaped Mixer with Recombinase Aided Amplification. BIOSENSORS 2022; 12:bios12090726. [PMID: 36140111 PMCID: PMC9496460 DOI: 10.3390/bios12090726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022]
Abstract
Foodborne pathogenic bacteria have become a worldwide threat to human health, and rapid and sensitive bacterial detection methods are urgently needed. In this study, a facile microfluidic chip was developed and combined with recombinase-aided amplification (RAA) for rapid and sensitive detection of Salmonella typhimurium using a non-contact eddy heater for dynamic lysis of bacterial cells and a 3D-printed fan-shaped active mixer for continuous-flow mixing. First, the bacterial sample was injected into the chip to flow through the spiral channel coiling around an iron rod under an alternating electromagnetic field, resulting in the dynamic lysis of bacterial cells by this non-contact eddy heater to release their nucleic acids. After cooling to ~75 °C, these nucleic acids were continuous-flow mixed with magnetic silica beads using the fan-shaped mixer and captured in the separation chamber using a magnet. Finally, the captured nucleic acids were eluted by the eluent from the beads to flow into the detection chamber, followed by RAA detection of nucleic acids to determine the bacterial amount. Under the optimal conditions, this microfluidic chip was able to quantitatively detect Salmonella typhimurium from 1.1 × 102 to 1.1 × 105 CFU/mL in 40 min with a detection limit of 89 CFU/mL and might be prospective to offer a simple, low-cost, fast and specific bacterial detection technique for ensuring food safety.
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Affiliation(s)
- Shangyi Wu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Hong Duan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Yingchao Zhang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Siyuan Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
| | - Lingyan Zheng
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, Beijing 100048, China
| | - Gaozhe Cai
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
- Correspondence: (J.L.); (X.Y.)
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: (J.L.); (X.Y.)
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22
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Chai Z, Soko WC, Xie J, Bi H. Microchip coupled with MALDI-TOF MS for the investigation of bacterial contamination of fish muscle products. Food Chem 2022; 396:133658. [PMID: 35841680 DOI: 10.1016/j.foodchem.2022.133658] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Bacterial contamination is a significant concern in food safety. Traditional methods, though being a gold standard for bacterial detection, are time-consuming. In this work, we managed to establish a simple and versatile magnetic-assisted microfluidic method for rapid bacterial detection of fish muscle products, by manipulating anti-human IgG functionalized magnetic beads in a zig-zag shaped microfluidic channel, increasing the probability for bacteria capture. The captured bacteria were characterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method is capable of isolating Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae from 5 μL of sablefish sarcoplasmic protein sample, and detecting Escherichia coli in the range of 6.0 to 6.0×104 CFU/mL with a detection limit of 6 CFU/mL. Bacterial growth on salmon sashimi during its period of storage was successfully monitored. The current protocol holds great potential for pathogen detection and microbial control in the food industry.
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Affiliation(s)
- Zhaoliang Chai
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, Shanghai 201306, China
| | - Winnie C Soko
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, Shanghai 201306, China
| | - Jing Xie
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, Shanghai 201306, China.
| | - Hongyan Bi
- College of Food Science and Engineering, Shanghai Ocean University, Hucheng Ring Road 999, Pudong New District, Shanghai 201306, China.
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23
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Qu G, Li Y, Zhao Z, Miao L, Wei F, Tang N, Xu Q, Nair V, Yao Y, Shen Z. Establishment and Application of a Real-Time Recombinase Polymerase Amplification Assay for the Detection of Avian Leukosis Virus Subgroup J. Front Vet Sci 2022; 9:847194. [PMID: 35873679 PMCID: PMC9301284 DOI: 10.3389/fvets.2022.847194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Avian leukosis caused by avian leukosis virus (ALV), belonging to the genus Alpharetrovirus of the family Retroviridae, is associated with benign and malignant tumors in hemopoietic cells in poultry. Although several methods have been developed for ALV detection, most of them are not suitable for rapid on-site testing due to instrument limitations, professional operators, or the low sensitivity of the method. Herein, we described the real-time recombinase polymerase amplification (RPA) assay for rapid detection of ALV subgroup J (ALV-J). The major viral structural glycoprotein gp85, highly specific for the subgroup, was used as the molecular target for the real-time RPA assay. The results were obtained at 38°C within 20 min, with the detection sensitivity of 10 copies/μl of standard plasmid pMD18-T-gp85 as the template per reaction. Real-time RPA was capable of ALV-J-specific detection without cross-reaction with other non-targeted avian pathogens. Of the 62 clinical samples tested, the ALV-positive rates of real-time RPA, PCR, and real-time PCR were 66.13% (41/62), 59.68% (37/62), and 67.74% (42/62), respectively. The diagnostic agreement between real-time RPA and real-time PCR was 98.39% (61/62), and the kappa value was 0.9636. The developed real-time ALV-J assay seems promising for rapid and sensitive detection of ALV-J in diagnostic laboratories. It is suitable for on-site detection, especially in a poor resource environment, thus facilitating the prevention and control of ALV-J.
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Affiliation(s)
- Guanggang Qu
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- *Correspondence: Guanggang Qu
| | - Yun Li
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Zhongwei Zhao
- Shandong Lvdu Biotechnology Co., Ltd, Binzhou, China
| | - Lizhong Miao
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Feng Wei
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Na Tang
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Qingqing Xu
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Guildford, United Kingdom
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Guildford, United Kingdom
- Yongxiu Yao
| | - Zhiqiang Shen
- Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, China
- Shandong Lvdu Biotechnology Co., Ltd, Binzhou, China
- Zhiqiang Shen
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24
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Hou L, Li D, Zhang N, Zhao J, Zhao Y, Sun X. Development of an isothermal recombinase-aided amplification assay for the rapid and visualized detection of Klebsiella pneumoniae. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3879-3886. [PMID: 34936095 DOI: 10.1002/jsfa.11737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Klebsiella pneumoniae is a zoonotic opportunistic pathogen, leading to severe infections in dairy cows and humans. Efficient, on-site and accurate detection of K. pneumoniae is necessary to reduce the harm of cow mastitis and human infections. The objective of this study was to establish a recombinase-aided amplification (RAA) method combined with lateral flow dipstick (LFD) for rapid detection of K. pneumoniae. RESULTS The primer concentration, incubation temperature and incubation time of the RAA reaction were optimized. When the primer concentration was 100 nmol L-1 , the strongest band could be obtained by incubation at 37 °C for 20 min. The RAA-LFD method had high specificity to K. pneumoniae and showed no cross-reaction with other pathogens. In addition, the detection limit of RAA-LFD for K. pneumoniae was 20 fg genomic DNA and 2.5 × 102 CFU mL-1 of bacteria in pure culture, which is 100 times higher than that of polymerase chain reaction (PCR) detection. Moreover, the RAA-LFD method can detect K. pneumoniae at initial concentrations as low as 2.5 CFU per 25 mL in artificially spiked milk samples after at least incubation for 6 h. Importantly, RAA-LFD had a high agreement with a test accuracy of 96.9%, compared with the biochemical identification method. Also, the detection accuracy of RAA-LFD was higher than that of the PCR assay (95.3%). CONCLUSIONS The results demonstrated that the RAA-LFD assay is an accurate, sensitive, simple and point-of-use detection method for K. pneumoniae, which could be used as a potential application in the research laboratory and for disease diagnosis. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Laiwang Hou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Darong Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Ni Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Jiayi Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, People's Republic of China
| | - Xiaohong Sun
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, People's Republic of China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, People's Republic of China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, People's Republic of China
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25
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Xiao F, Liu J, Feng X, Xie G, Zhang W, Xu H. Rapid enrichment and detection of Staphylococcus aureus in milk using polyethyleneimine functionalized magnetic nanoparticles. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Feng X, Zhou D, Xie G, Liu J, Xiong Q, Xu H. A novel photoreactive DNA-binding dye for detecting viable Klebsiella pneumoniae in powdered infant formula. J Dairy Sci 2022; 105:4895-4902. [PMID: 35450718 DOI: 10.3168/jds.2022-21900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/23/2022] [Indexed: 11/19/2022]
Abstract
In addition to Cronobacter spp., Klebsiella pneumoniae is another opportunistic bacterial pathogen present in powdered infant formula (PIF) that can cause pneumonia, septicemia, and other diseases. In this study, a rapid and specific method based on a fluorescence probe was developed for detecting viable K. pneumoniae in PIF samples via the combination of recombinase-aided amplification (RAA) with thiazole orange monoazide (TOMA) dye (the TOMA-RAA assay hereafter). As a novel photosensitive DNA-intercalating dye, TOMA was used to penetrate bacterial cells, including both dead and viable cells, as verified by confocal laser scanning microscopy and fluorescent emission spectrometry. Importantly, the RAA assay exhibited good performance in detecting K. pneumoniae within 40 min at 39°C. Under optimal conditions, the TOMA-RAA assay can detect as low as 2.6 × 103 cfu/mL of K. pneumoniae in pure culture and 2.3 × 104 cfu/g of K. pneumoniae in spiked PIF sample. After 3 h of pre-enrichment, 3 × 100 cfu/g of K. pneumoniae can be detected. Furthermore, the TOMA-RAA assay displayed an excellent anti-interference ability to nontarget bacteria. In short, the proposed method has great potential application for the rapid and accurate detection of viable K. pneumoniae in PIF.
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Affiliation(s)
- Xiaoyan Feng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, P.R. China
| | - Donggen Zhou
- Ningbo International Travel Healthcare Center (Ningbo Customs Port Outpatient Department), Ningbo, 315010, P.R. China
| | - Guoyang Xie
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, P.R. China
| | - Ju Liu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, P.R. China
| | - Qin Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, P.R. China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, P.R. China.
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27
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Zhao J, Li Y, Xue Q, Zhu Z, Zou M, Fang F. A novel rapid visual detection assay for Toxoplasma gondii combining recombinase-aided amplification and lateral flow dipstick coupled with CRISPR-Cas13a fluorescence (RAA-Cas13a-LFD). Parasite 2022; 29:21. [PMID: 35420541 PMCID: PMC9009239 DOI: 10.1051/parasite/2022021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
Toxoplasmosis, a parasitic disease resulting from Toxoplasma gondii infection, remains prevalent worldwide, and causes great harm to immunodepressed patients, pregnant women and newborns. Although various molecular approaches to detect T. gondii infection are available, they are either costly or technically complex. This study aimed at developing a rapid visual detection assay using recombinase-aided amplification (RAA) and lateral flow dipstick (LFD) coupled with CRISPR-Cas13a fluorescence (RAA-Cas13a-LFD) to detect T. gondii. The RAA-Cas13a-LFD assay was performed in an incubator block at 37 °C within 2 h, and the amplification results were visualized and determined through LFD by the naked eye. The detection limit was 1 × 10-6 ng/μL by our developed RAA-Cas13a-LFD protocol, 100-fold higher than that by qPCR assay (1 × 10-8 ng/μL). No cross-reaction occurred either with the DNA of human blood or Ascaris lumbricoides, Digramma interrupta, Entamoeba coli, Fasciola gigantica, Plasmodium vivax, Schistosoma japonicum, Taenia solium, and Trichinella spiralis, and the positive rate by RAA-Cas13a-LFD assay was identical to that by qPCR assay (1.50% vs. 1.50%) in detecting T. gondii infection in the unknown blood samples obtained from clinical settings. Our findings demonstrate that this RAA-Cas13a-LFD assay is not only rapid, sensitive, and specific and allows direct visualization by the naked eye, but also eliminates sophisticated and costly equipment. More importantly, this technique can be applied to on-site surveillance of T. gondii.
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Affiliation(s)
- Jinhong Zhao
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China - Provincial Key Laboratory of Active Biological Macro-Molecules, Wuhu 241002, Anhui, China
| | - Yuanyuan Li
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Qiqi Xue
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Zhiwei Zhu
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Minghui Zou
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Fang Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China
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28
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Fan Z, Feng Y, Xu W, Feng J, Yan C, Fu T, Zhao H, Cui J, Gan L, Liu S, Du S, Zhang R, Xu Z, Li N, Xue G, Yuan J. Rapid Detection of Multi-Resistance Strains Carrying mcr-1 Gene Using Recombinase-Aided Amplification Directly on Clinical Samples. Front Microbiol 2022; 13:852488. [PMID: 35432248 PMCID: PMC9009391 DOI: 10.3389/fmicb.2022.852488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
With the increasingly severe problem of bacterial resistance, colistin, as the last line of defense, has attracted attention again. Mobile colistin resistance (mcr-1) gene is involved in the horizontal transmission of colistin resistance in Gram-negative bacteria (GNB), which is a serious threat to human health. Therefore, rapid detection of mcr-1 gene presence in clinical samples is crucial. In this study, a Recombinase-aided amplification(RAA) method for mcr-1 was successfully constructed, with sensitivity of 20 copies/reaction. In addition, amplification signal could only be detected in the strain containing mcr-1 gene among 14 different bacterial species. The method was then used to test a total of 672 clinical samples from a pediatric hospital in Beijing. Five strains harbored mcr-1 genes were isolated from mcr-1-positive clinical samples and identified as Escherichia coli. Multi-locus sequence typing (MLST) analysis showed that the five E. coli belonged to different ST types. Notably, the mcr-1 gene from the isolates could be transferred conjugately to the recipient strain E. coli J53, with highest transfer efficiency up to 57–58%, suggesting that the mcr-1 gene was located on the plasmid. These findings showed that the RAA assay has potential to be a rapid and sensitive mcr-1 gene screening test for clinical samples, and mcr-1 could be transmitted vertically and horizontally between and within bacterial species in a plasmid-mediated manner.
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Affiliation(s)
- Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Wenjian Xu
- Children’s Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- 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
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shiyu Liu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Nannan Li
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- *Correspondence: Guanhua Xue,
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- Jing Yuan,
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Gu K, Song Z, Zhou C, Ma P, Li C, Lu Q, Liao Z, Huang Z, Tang Y, Li H, Zhao Y, Yan W, Lei C, Wang H. Development of nanobody-horseradish peroxidase-based sandwich ELISA to detect Salmonella Enteritidis in milk and in vivo colonization in chicken. J Nanobiotechnology 2022; 20:167. [PMID: 35361208 PMCID: PMC8973953 DOI: 10.1186/s12951-022-01376-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/14/2022] [Indexed: 02/08/2023] Open
Abstract
Background Salmonella Enteritidis (S. Enteritidis) being one of the most prevalent foodborne pathogens worldwide poses a serious threat to public safety. Prevention of zoonotic infectious disease and controlling the risk of transmission of S. Enteriditidis critically requires the evolution of rapid and sensitive detection methods. The detection methods based on nucleic acid and conventional antibodies are fraught with limitations. Many of these limitations of the conventional antibodies can be circumvented using natural nanobodies which are endowed with characteristics, such as high affinity, thermal stability, easy production, especially higher diversity. This study aimed to select the special nanobodies against S. Enteriditidis for developing an improved nanobody-horseradish peroxidase-based sandwich ELISA to detect S. Enteritidis in the practical sample. The nanobody-horseradish peroxidase fusions can help in eliminating the use of secondary antibodies labeled with horseradish peroxidase, which can reduce the time of the experiment. Moreover, the novel sandwich ELISA developed in this study can be used to detect S. Enteriditidis specifically and rapidly with improved sensitivity. Results This study screened four nanobodies from an immunized nanobody library, after four rounds of screening, using the phage display technology. Subsequently, the screened nanobodies were successfully expressed with the prokaryotic and eukaryotic expression systems, respectively. A sandwich ELISA employing the SE-Nb9 and horseradish peroxidase-Nb1 pair to capture and to detect S. Enteritidis, respectively, was developed and found to possess a detection limit of 5 × 104 colony forming units (CFU)/mL. In the established immunoassay, the 8 h-enrichment enabled the detection of up to approximately 10 CFU/mL of S. Enteriditidis in milk samples. Furthermore, we investigated the colonization distribution of S. Enteriditidis in infected chicken using the established assay, showing that the S. Enteriditidis could subsist in almost all parts of the intestinal tract. These results were in agreement with the results obtained from the real-time PCR and plate culture. The liver was specifically identified to be colonized with quite a several S. Enteriditidis, indicating the risk of S. Enteriditidis infection outside of intestinal tract. Conclusions This newly developed a sandwich ELISA that used the SE-Nb9 as capture antibody and horseradish peroxidase-Nb1 to detect S. Enteriditidis in the spike milk sample and to analyze the colonization distribution of S. Enteriditidis in the infected chicken. These results demonstrated that the developed assay is to be applicable for detecting S. Enteriditidis in the spiked milk in the rapid, specific, and sensitive way. Meanwhile, the developed assay can analyze the colonization distribution of S. Enteriditidis in the challenged chicken to indicate it as a promising tool for monitoring S. Enteriditidis in poultry products. Importantly, the SE-Nb1-vHRP as detection antibody can directly bind S. Enteritidis captured by SE-Nb9, reducing the use of commercial secondary antibodies and shortening the detection time. In short, the developed sandwich ELISA ushers great prospects for monitoring S. Enteritidis in food safety control and further commercial production. Graphic Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-022-01376-y.
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Affiliation(s)
- Kui Gu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Zengxu Song
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Changyu Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Peng Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Chao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Qizhong Lu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziwei Liao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Zheren Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Yizhi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Hao Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Yu Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Wenjun Yan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China. .,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People's Republic of China. .,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
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30
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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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31
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Feng ZS, Li JY, Zhang JY, Li FY, Guan HX, Zhang RQ, Liu H, Guo Q, Shen XX, Kan B, Ma XJ. Development and evaluation of a sensitive recombinase aided amplification assay for rapid detection of Vibrio parahaemolyticus. J Microbiol Methods 2022; 193:106404. [PMID: 34990645 DOI: 10.1016/j.mimet.2021.106404] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/27/2022]
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is a widely distributed pathogen in the coastal areas, which causes food poisoning and leads to gastroenteritis and sepsis. Therefore, developing a simple, sensitive, and rapid detection method for V. parahaemolyticus is a major concern globally. This study established a sensitive and rapid technique based on recombinase aided amplification (RAA) to detect V. parahaemolyticus. The RAA reaction was carried out successfully at 39 °C within 30 min. The sensitivity of the RAA assay was 101 copies/μL using the recombinant plasmid and 10-3 ng/μL using the V. parahaemolyticus strain. In addition, RAA directly detected 7 × 103 CFU/mL of simulated fecal samples and 0.1 CFU/mL after enrichment for 4 h. The sensitivity and specificity of the RAA assay using fecal and fish samples were 100% similar to that of the real-time PCR. We conclude that the RAA assay is an ideal screening method for detecting V. parahaemolyticus due to its rapidity, high accuracy, and simplicity in operation.
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Affiliation(s)
- Zhi-Shan Feng
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, Hebei, China
| | - Jing-Yi Li
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, 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 102206, China
| | - Jing-Yun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute forCommunicable DiseaseControl and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Feng-Yu Li
- Hebei Medical University, Shijiazhuang 050031, Hebei, China; Hebei General Hospital, Shijiazhuang 050070, 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 102206, China
| | - Hong-Xia Guan
- Wuxi Center for Disease Control and Prevention, Wuxi 214023, Jiangsu, China
| | - Rui-Qing Zhang
- 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 102206, China.
| | - Hong Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences and Medicine, Shandong University of Technology, Zibo255049, Shandong, China
| | - Qi Guo
- Laboratory of Virology, Beijing Key Laboratory ofEtiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing 100020, 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 102206, China.
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute forCommunicable DiseaseControl and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, 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 102206, China.
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32
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Wang S, Cai G, Duan H, Qi W, Lin J. Automatic and multi-channel detection of bacteria on a slidable centrifugal disc based on FTA card nucleic acid extraction and recombinase aided amplification. LAB ON A CHIP 2021; 22:80-89. [PMID: 34796896 DOI: 10.1039/d1lc00915j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Rapid screening of foodborne pathogens is key to preventing food poisoning. In this study, a slidable centrifugal disc was developed for automatic and multi-channel detection of Salmonella typhimurium using Flinders Technology Associates (FTA) cards for nucleic acid extraction and recombinase aided amplification (RAA) for nucleic acid detection. The slidable FTA switching and centrifugal fluidic control were elaborately combined to achieve fully automatic operations, including centrifugation of the bacterial sample to obtain the concentrated bacteria, heating and drying of the FTA card to extract the nucleic acids, washing of the FTA card to remove the impurities, and RAA detection of the extracted DNA to determine the concentration. Under the optimal conditions, this slidable centrifugal disc was able to detect 10 CFU mL-1 in a spiked chicken meat supernatant in 1 h with an average recovery of 101.8% and an average standard deviation of 6.5%. This disc has been demonstrated as an alternative for sample-in-result-out detection of Salmonella and has shown potential for simultaneous detection of multiple bacteria.
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Affiliation(s)
- Siyuan Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China.
- Key Laboratory of Modern Precision Agriculture System Integration Research, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Gaozhe Cai
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Hong Duan
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China.
| | - Wuzhen Qi
- Key Laboratory of Modern Precision Agriculture System Integration Research, Ministry of Education, China Agricultural University, Beijing 100083, China
| | - Jianhan Lin
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China.
- Key Laboratory of Modern Precision Agriculture System Integration Research, Ministry of Education, China Agricultural University, Beijing 100083, China
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33
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Wang W, Zhou L, Ge X, Han J, Guo X, Chen Y, Zhang Y, Yang H. Development of a VP2-based real-time fluorescent reverse transcription recombinase-aided amplification assay to rapidly detect Senecavirus A. Transbound Emerg Dis 2021; 69:2828-2839. [PMID: 34931455 DOI: 10.1111/tbed.14435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 01/28/2023]
Abstract
Senecavirus A (SVA), a newly emergent picornavirus correlated with sudden neonatal mortality and vesicular lesions in pigs, has had a considerable impact on the global pig farming industry. Timely and dependable detection of SVA is helpful in preventing the further spread of this pathogenic virus. In the current study, a real-time fluorescent reverse transcription recombinase-aided amplification (rRT-RAA) assay, which targets the most conserved region within the VP2 gene of SVA, was developed and evaluated for SVA detection. The detection limit for this assay was tested to be 1.185 50% tissue culture infective dose (TCID50 ) of SVA RNA per reaction at a 95% confidence interval, which is comparable to that of a previously published rRT-PCR assay for SVA. The testing results of the rRT-RAA assay were very reproducible and repeatable, with inter- and intra-assay coefficient of variation values less than 7.0%. In addition, the established rRT-RAA assay displayed excellent specificity for SVA detection without cross-reaction with other clinically important swine pathogenic viruses. The diagnostic performance of rRT-RAA was evaluated using 189 clinical swine samples, which were detected in parallel using the reference rRT-PCR assay. The results showed that 146 and 151 samples tested positive for SVA by rRT-RAA and rRT-PCR, respectively. The overall agreement between both assays was 97.4% (184/189) with a kappa value of 0.927 (p < .001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9192, p < .0001). Taken together, our newly established rRT-RAA assay is a powerful and time-saving diagnostic tool for SVA detection in clinical samples. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wenlong Wang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Yanhong Chen
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, P.R. China
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34
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Chen H, Sun C, Wang Y, Gao X, You J, Yu W, Sun N, Yang Y, Li X. Rapid Detection of SARS-CoV-2 Using Duplex Reverse Transcription-Multienzyme Isothermal Rapid Amplification in a Point-of-Care Testing. Front Cell Infect Microbiol 2021; 11:678703. [PMID: 34746020 PMCID: PMC8569318 DOI: 10.3389/fcimb.2021.678703] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 09/30/2021] [Indexed: 12/12/2022] Open
Abstract
In December 2019, a severe acute respiratory syndrome caused by SARS-CoV-2 spread rapidly worldwide. Portable nucleic acid tests of SARS-CoV-2 are critically important for diagnostics. In this study, we used an isothermal amplification method-Multienzyme Isothermal Rapid Amplification (MIRA)-for rapid detection of SARS-CoV-2. We designed the primers and probes in ORF1ab and N gene of SARS-CoV-2. The amplicons could be monitored by lateral flow dipsticks (LFDs). The reaction temperature, time, concentrations of primers and probes, and working volume were optimized. Four commercial swab collection buffers were used to test the amplification efficacy of our assay without RNA extraction. Our assay was able to amplify duplex targets of SARS-CoV-2 in one single reaction using one-step RT-MIRA. The assay worked well in a low volume of 10 μl at 38°C for 20 min. Using three collection buffers without guanidinium, our assay was able to amplify efficaciously without RNA extraction. The 95% limit of detection (LoD) of the RT-MIRA assay was 49.5 (95% CI, 46.8-52.7) copies/ml for ORF1ab gene and 48.8 (95% CI, 46.5-52.6) copies/ml for N gene. There is no cross-reaction with other human respiratory pathogens, such as SARS-CoV, MERS-CoV, influenza A virus, influenza B virus, human adenovirus, respiratory syncytial virus, human parainfluenza virus, and coronavirus 229E in our assay. The precision evaluation revealed that the C50-20% to C50+20% range bounds the C5-C95 interval. This assay also showed high anti-interference ability. The extraction-free RT-MIRA and qPCR detection results of 243 nucleic acid specimens from suspected patients or national references showed a 100.0% (95% confidence interval, 94.2%-100.0%) positive predictive value and a 100.0% (95% confidence interval, 92.7%-100.0%) negative predictive value. Compared with qPCR, the kappa value of the two assays was 1.00 (P < 0.0001). In conclusion, we provide a portable and visualized method for detection of SARS-CoV-2 without RNA extraction, allowing its application in SARS-CoV-2 on-site detection.
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Affiliation(s)
- Hui Chen
- Department of Medicine, JiangSu University, Zhenjiang, China.,Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Chang Sun
- Department of Orthopaedics, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Yang Wang
- Department of Orthopaedics, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Xiaojiao Gao
- Department of Clinical Laboratory, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Jinwei You
- Department of Laboratory Animal, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Wanwan Yu
- Department of Emergency, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Ning Sun
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Yang Yang
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China
| | - Xiaojun Li
- Department of Basic Medical Laboratory, Institute of Clinical Laboratory Science, Jinling Hospital, Clinical School of Medical College, Nanjing University, Nanjing, China.,State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, China
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35
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Mu D, Zhou D, Xie G, Liu J, Xiong Q, Feng X, Xu H. The fluorescent probe-based recombinase-aided amplification for rapid detection of Escherichia coli O157:H7. Mol Cell Probes 2021; 60:101777. [PMID: 34737039 DOI: 10.1016/j.mcp.2021.101777] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 01/21/2023]
Abstract
Escherichia coli O157:H7 (E. coli O157:H7) is a common foodborne morbigenous microorganism, which can spread through fecal-oral transmission. Humans can be infected by ingesting foods and water contaminated with E. coli O157:H7, which can cause various symptoms. In present study, we have successfully developed a quick and hypersensitive fluorescent probe-based Recombinase-aided amplification (RAA) method and applied in E. coli O157:H7 detection at 39 °C in 20 min. The sensitivity of the assay in pure E. coli O157:H7 suspension was 5.6 × 100 CFU/mL. The fluorescent probe-based RAA assay was further applied in three samples, and the limit of detection (LOD) in skimmed milk, lettuces and lake water was 5.4 × 101 CFU/mL, 7.9 × 101 CFU/mL and 5.2 × 101 CFU/mL, separately. This method showed a high sensitivity and short detection time, which has the feasible application in on-site test in real samples.
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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.
| | - Qin Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China.
| | - Xiaoyan Feng
- 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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36
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An B, Zhang H, Su X, Guo Y, Wu T, Ge Y, Zhu F, Cui L. Rapid and Sensitive Detection of Salmonella spp. Using CRISPR-Cas13a Combined With Recombinase Polymerase Amplification. Front Microbiol 2021; 12:732426. [PMID: 34733250 PMCID: PMC8558462 DOI: 10.3389/fmicb.2021.732426] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
Salmonella spp. is one of the most common foodborne disease-causing pathogens that can cause severe diseases in very low infectious doses. Rapid and sensitive detecting Salmonella spp. is advantageous to the control of its spread. In this study, a conserved short fragment of the Salmonella invA gene was selected and used to design primers and specific crRNA (CRISPR RNA) for establishing a one-tube and two-step reaction system for Salmonella spp. detection, by combining recombinase polymerase amplification (RPA) with CRISPR-Cas13a (Clustered Regularly Interspaced Short Palindromic Repeats associated protein 13a) cleavage. The established one-tube RPA-Cas13a method can complete the detection within 20 min and the two-step RPA-Cas13a method detection time within 45 min. The designed primers were highly specific to Salmonella spp. and had no cross-reaction with the other nine diarrheal bacteria. The one-tube RPA-Cas13a could detect the Salmonella genome with the limit of 102 copies, which was the same as real-time polymerase chain reaction (PCR), but less sensitive than two-step RPA-Cas13a (100 copies). The detection results of one-tube or two-step RPA-Cas13a and real-time PCR were highly consistent in clinical samples. One-tube RPA-Cas13a developed in this study provides a simple, rapid, and specific detection method for Salmonella spp. While two-step assay was more sensitive and suitable for samples at low abundance.
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Affiliation(s)
- Bailin An
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,College of Pharmacy, Nankai University, Tianjin, China
| | - Hongbin Zhang
- Jiangyin City Center for Disease Control and Prevention, Wuxi, China
| | - Xuan Su
- College of Pharmacy, Nankai University, Tianjin, China
| | - Yue Guo
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tao Wu
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yiyue Ge
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Fengcai Zhu
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Lunbiao Cui
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
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37
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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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38
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Yu S, Xu Q, Huang J, Yi B, Aguilar ZP, Xu H. Rapid and sensitive detection of Salmonella in milk based on hybridization chain reaction and graphene oxide fluorescence platform. J Dairy Sci 2021; 104:12295-12302. [PMID: 34538487 DOI: 10.3168/jds.2021-20713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022]
Abstract
Salmonella is a foodborne pathogen that has contributed to numerous food safety accidents worldwide, making it necessary to detect contamination at an early stage. A pair of specific primers based on the invA gene of Salmonella was designed for PCR. Target double-stranded DNA (dsDNA) from PCR was purified and denatured at high temperature to obtain target single-stranded DNA (ssDNA). Two carboxyfluorescein-labeled hairpin probes (H1-FAM and H2-FAM) were designed with complementary portions to the ssDNA sequence so that binding could trigger H1-FAM and H2-FAM hybridization chain reaction (HCR) to produce a long dsDNA complex. In this study, graphene oxide (GO) was used in the development of a homogeneous fluorescence detection platform for Salmonella. Using this HCR-GO assay platform, Salmonella detection was completed in 3.5 h. Salmonella was reliably and specifically detected with a limit of detection (LOD) of 4.2 × 101 cfu/mL in pure culture. Moreover, this new HCR-GO assay platform was successfully applied to the detection of Salmonella in artificially contaminated milk with a LOD of 4.2 × 102 cfu/mL.
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Affiliation(s)
- Shuang Yu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Qian Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Jin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, PR China
| | - Bo Yi
- 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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39
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Yang M, Tang Y, Qi L, Zhang S, Liu Y, Lu B, Yu J, Zhu K, Li B, Du Y. SARS-CoV-2 Point-of-Care (POC) Diagnosis Based on Commercial Pregnancy Test Strips and a Palm-Size Microfluidic Device. Anal Chem 2021; 93:11956-11964. [PMID: 34424659 PMCID: PMC8406982 DOI: 10.1021/acs.analchem.1c01829] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/09/2021] [Indexed: 12/19/2022]
Abstract
Coronavirus diseases such as the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), pose serious threats. Portable and accurate nucleic acid detection is still an urgent need to achieve on-site virus screening and timely infection control. Herein, we have developed an on-site, semiautomatic detection system, aiming at simultaneously overcoming the shortcomings suffered by various commercially available assays, such as low accuracy, poor portability, instrument dependency, and labor intensity. Ultrasensitive isothermal amplification [i.e., reverse transcription loop-mediated isothermal amplification (RT-LAMP)] was applied to generate intensified SARS-CoV-2 RNA signals, which were then transduced to portable commercial pregnancy test strips (PTSs) via ultraspecific human chorionic gonadotropin (hCG)-conjugated toehold-mediated strand exchange (TMSE) probes (hCG-P). The entire detection was integrated into a four-channel, palm-size microfluidic device, named the microfluidic point-of-care (POC) diagnosis system based on the PTS (MPSP) detection system. It provides rapid, cost-effective, and sensitive detection, of which the lowest concentration of detection was 0.5 copy/μL of SARS-CoV-2 RNA, regardless of the presence of other similar viruses, even highly similar severe acute respiratory syndrome coronavirus (SARS-CoV). The successful detection of the authentic samples from different resources evaluated the practical application. The commercial PTS provides a colorimetric visible signal, which is instrument- and optimization-free. Therefore, this MPSP system can be immediately used for SARS-CoV-2 emergency detection, and it is worthy of further optimization to achieve full automation and detection for other infectious diseases.
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Affiliation(s)
- Meiting Yang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
| | - Yidan Tang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
| | - Lijuan Qi
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
- Department
of Chemistry, University of Science &
Technology of China, Hefei 230026, Anhui, China
| | - Sicai Zhang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
| | - Yichen Liu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
- Department
of Chemistry, University of Science &
Technology of China, Hefei 230026, Anhui, China
| | - Baiyang Lu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
| | - Jiaxue Yu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
| | - Kun Zhu
- Proteinbiosen
Biotechnology Limited Liability Company, Beijing 100000, P.R. China
| | - Bingling Li
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
- Department
of Chemistry, University of Science &
Technology of China, Hefei 230026, Anhui, China
| | - Yan Du
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of
Sciences, Changchun 130022, Jilin, P. R.
China
- Department
of Chemistry, University of Science &
Technology of China, Hefei 230026, Anhui, China
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40
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He Y, Chen W, Fan J, Fan S, Ding H, Chen J, Yi L. Recombinase-Aided Amplification Coupled with Lateral Flow Dipstick for Efficient and Accurate Detection of Porcine Parvovirus. Life (Basel) 2021; 11:life11080762. [PMID: 34440506 PMCID: PMC8401844 DOI: 10.3390/life11080762] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/12/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Porcine parvovirus (PPV) infection is the primary cause of SMEDI (stillbirth; mummification; embryonic death; infertility) syndrome, which is a global burden for the swine industry. Thus, it is crucial to establish a rapid and efficient detection method against PPV infection. In the present work, we developed a recombinase-aided amplification (RAA) assay, coupled with a lateral flow dipstick (LFD), to achieve an amplification of PPV DNA at 37 °C within 15 min. The detection limits of PPV RAA-LFD assay were 102 copies/μL recombinant plasmid pMD19-T-VP1, 6.38 × 10-7 ng/μL PPV DNA, and 10-1 TCID50/mL virus, respectively. This method was highly specific for PPV detection with no cross-reactivity for other swine pathogens. In contrast to polymerase chain reaction (PCR), the PPV RAA-LFD assay is more sensitive and cost-saving. Hence, the established PPV RAA-LFD assay provided an alternative for PPV detection, especially in resource-limited regions.
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Affiliation(s)
- Yihong He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
| | - Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Jindai Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (J.C.); (L.Y.)
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (W.C.); (J.F.); (S.F.); (H.D.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (J.C.); (L.Y.)
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41
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Feng Y, Xue G, Feng J, Yan C, Cui J, Gan L, Zhang R, Zhao H, Xu W, Li N, Liu S, Du S, Zhang W, Yao H, Tai J, Ma L, Zhang T, Qu D, Wei Y, Yuan J. Rapid Detection of New Delhi Metallo-β-Lactamase Gene Using Recombinase-Aided Amplification Directly on Clinical Samples From Children. Front Microbiol 2021; 12:691289. [PMID: 34367092 PMCID: PMC8339468 DOI: 10.3389/fmicb.2021.691289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/30/2021] [Indexed: 11/26/2022] Open
Abstract
New Delhi metallo-β-lactamase, a metallo-β-lactamase carbapenemase type, mediates resistance to most β-lactam antibiotics including penicillins, cephalosporins, and carbapenems. Therefore, it is important to detect blaNDM genes in children’s clinical samples as quickly as possible and analyze their characteristics. Here, a recombinase-aided amplification (RAA) assay, which operates in a single one-step reaction tube at 39°C in 5−15 min, was established to target blaNDM genes in children’s clinical samples. The analytical sensitivity of the RAA assay was 20 copies, and the various bacterial types without blaNDM genes did not amplify. This method was used to detect blaNDM genes in 112 children’s stool samples, 10 of which were tested positive by both RAA and standard PCR. To further investigate the characteristics of carbapenem-resistant bacteria carrying blaNDM in children, 15 carbapenem-resistant bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Citrobacter freundii, Klebsiella oxytoca, Acinetobacter junii, and Proteus mirabilis) were isolated from the 10 samples. Notably, more than one bacterial type was isolated from three samples. Most of these isolates were resistant to cephalosporins, cefoperazone-sulbactam, piperacillin-tazobactam, ticarcillin-clavulanic acid, aztreonam, co-trimoxazole, and carbapenems. blaNDM–1 and blaNDM–5 were the two main types in these samples. These data show that the RAA assay has potential to be a sensitive and rapid blaNDM gene screening test for clinical samples. The common existence of blaNDM and multi-drug resistance genes presents major challenges for pediatric treatment.
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Affiliation(s)
| | - Guanhua Xue
- Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Hanqin Zhao
- Capital Institute of Pediatrics, Beijing, China
| | - Wenjian Xu
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Nannan Li
- Capital Institute of Pediatrics, Beijing, China
| | - Shiyu Liu
- Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Capital Institute of Pediatrics, Beijing, China
| | | | - Hailan Yao
- Capital Institute of Pediatrics, Beijing, China
| | - Jun Tai
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Lijuan Ma
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Dong Qu
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Yongxiang Wei
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Capital Institute of Pediatrics, Beijing, China
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42
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Tu F, Zhang Y, Xu S, Yang X, Zhou L, Ge X, Han J, Guo X, Yang H. Detection of pseudorabies virus with a real-time recombinase-aided amplification assay. Transbound Emerg Dis 2021; 69:2266-2274. [PMID: 34273259 DOI: 10.1111/tbed.14241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/04/2021] [Accepted: 07/08/2021] [Indexed: 11/27/2022]
Abstract
Pseudorabies (PR) is an acute infectious disease of pigs caused by pseudorabies virus (PRV), which has caused great economic losses to the pig industry worldwide. Reliable and timely diagnose is crucial for the surveillance, control and eradication of PR. Here, a real-time fluorescent recombinase-aided amplification (real-time RAA) assay was established to detect PRV. Primers and probes were designed based on the conserved regions of the PRV gE gene. The assay was specific for the detection of wild-type PRV, showing no cross-reactivity with other important porcine viruses (including PRV gE-deleted vaccine strains). Analytical sensitivity of the assay was three 50% tissue culture infectious doses (TCID50 ) of PRV DNA per reaction with 95% reliability, which is comparable to that of a PRV-specific real-time PCR (qPCR) assay. In diagnosis of 206 clinical tissue samples, the diagnose accordance rate between the real-time RAA assay and qPCR assay was 97.57% (201/206). Interestingly, the amplified products of real-time RAA could be visualized under a portable blue light instrument, making it possible for the rapid detection of PRV in resource-limited settings and on-site screening. Therefore, our developed real-time RAA assay is a diagnostic method for the rapid detection of PRV in the field.
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Affiliation(s)
- Fei Tu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Yongning Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Shengkui Xu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Xintan Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, P. R. China
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43
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Zhao J, Ao C, Wan Z, Dzakah EE, Liang Y, Lin H, Wang H, Tang S. A point-of-care rapid HIV-1 test using an isothermal recombinase-aided amplification and CRISPR Cas12a-mediated detection. Virus Res 2021; 303:198505. [PMID: 34271038 DOI: 10.1016/j.virusres.2021.198505] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/26/2022]
Abstract
Human immunodeficiency virus type one (HIV-1) infection is one of the major public health problems worldwide. Effective control of HIV-1 epidemic relies on early diagnosis of HIV-1 infection by using simple, rapid point-of-care test (POCT). An integrated assay was developed and evaluated in this study to combine a real-time isothermal reverse-transcription recombinase-aided amplification (rRT-RAA) and CRISPR Cas12a-mediated detection for HIV-1. The testing results could be directly observed with naked eye using a blue light imager, making it a suitable on-site testing assay. Our preliminary data indicated that the assay was capable of detecting 20 copies of purified HIV-1 DNA or RNA per reaction or as low as 123 copies/ml of HIV-1 viral load in clinical samples. When screening 155 clinical samples with or without HIV-1 infection, the sensitivity and specificity of the rRT-RAA assay were 98.95% (94/95) and 100% (60/60), respectively. The coefficient value was 0.986 when compared with the Chinese FDA approved HIV-1 RT-qPCR assay. Furthermore, the newly developed HIV-1 rRT-RAA assay could detect the major HIV-1 genotypes CRF01_AE, CRF07_BC, CRF08_BC, CRF08_BC and subtype B in China. Our preliminary results indicated that the rRT-RAA assay or its combination with CRISPR Cas12a-mediated detection could serve as a rapid, convenient, and robust assay for HIV-1 detection.
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Affiliation(s)
- Jianhui Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Cailing Ao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zhengwei Wan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Emmanuel Enoch Dzakah
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Yuanhao Liang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Hongqing Lin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Haiying Wang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Shixing Tang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; Wenzhou Institute, University of Chinese Academy of Sciences, China.
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44
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He Z, Tong Z, Tan B, He X, Zhang T, Guo Y, Jin L, He N, Li S, Chen Z. Rapid Detection of DNA Methylation with a Novel Real-Time Fluorescence Recombinase-Aided Amplification Assay. J Biomed Nanotechnol 2021; 17:1364-1370. [PMID: 34446139 DOI: 10.1166/jbn.2021.3111] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Researchers have conducted in-depth research on DNA methylation mechanism, which is related to various diseases such as deficiency of imprinted gene and occurrence of tumors. This study provides a novel rapid quantitative detection assay and real-time fluorescence recombinase-aided amplification assay (RAA) for DNA methylation. Firstly, specific sequence of methylation genes was chosen and primers and fluorogenic probe for RAA experiment were designed and synthesized. Lastly, these amplification products were proven by sequencing and analysis. Results showed that the amplification efficiency and template concentration of RAA had linear dependent (R² > 95%) when the concentration range was 4.64×108 copies/μL˜4.64×10⁴ copies/μL. The test assay can also detect positive samples when the template concentration is below 4.64×10⁴ copies/μL. Remarkably, the entire experiment process only takes 15-20 minutes, so it is beneficial for rapid bedside simple screening of some special DNA methylation sites, such as detection of resistance genes. In a word, this method has very great potential for diseases with DNA methylation in clinical settings, especially if methylation analysis needs to be done quickly and easily.
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Affiliation(s)
- Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Zengrui Tong
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Boyu Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Xuliang He
- Department of General Surgery, People's Hospital of Zhuzhou City Affiliated to Changsha Medical College, Zhuzhou 412011, P. R. China
| | - Tao Zhang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Yuan Guo
- Department of Laboratory, Central Hospital of Zhuzhou City, Zhuzhou 412007, P. R. China
| | - Lian Jin
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
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45
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Chen W, Fan J, Li Z, Zhang Y, Qin Y, Wu K, Li X, Li Y, Fan S, Zhao M. Development of Recombinase Aided Amplification Combined With Disposable Nucleic Acid Test Strip for Rapid Detection of Porcine Circovirus Type 2. Front Vet Sci 2021; 8:676294. [PMID: 34250063 PMCID: PMC8267240 DOI: 10.3389/fvets.2021.676294] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Porcine circovirus type 2 (PCV2) is the dominant causative agent of PCV2 systemic disease (PCV2-SD) in pigs. It can also associate with other diseases such as respiratory and enteric diseases, reproductive failure, porcine dermatitis and nephropathy syndrome in pigs. Currently, PCV2 infection is a considerable threat in the swine industry. Therefore, it is of great significance to prevent, control, and accurately detect PCV2 in pig farms. Recombinase aided amplification (RAA) technology is an isothermal nucleic acid amplification technology that could rapidly amplify the target gene fragment at a constant temperature. The amplification products labeled with specific molecules could be visually detected using the test strip with the corresponding antibody. In the present study, the RAA technology combined with a nucleic acid test strip (RAA-strip) was established for simple and specific detection of PCV2. Primers and probes targeting the PCV2 ORF2 gene were designed according to the RAA technology principles. The PCV2 RAA-strip established in this study could detect as low as 103 copies/μL of recombinant plasmids containing the PCV2 ORF2 gene fragment. The lowest detection limit about viral DNA and virus titers was 6.7 × 10-6 ng/μL and 10 TCID50/mL, respectively. Furthermore, no cross-reaction with other porcine viruses occurred at 37°C and within 15 min. We used 42 clinical samples to assess the performance of our established method. The positive rate of clinical samples detected by PCV2 RAA-strip was 50.00%. This was similar to that detected by PCV2 PCR (45.24%). In conclusion, due to the advantages of strong specificity, high sensitivity, excellent reproducibility, and simple operation method, our PCV2 RAA-strip is suitable for the rapid clinical detection of PCV2 on-site.
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Affiliation(s)
- Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Jindai Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuanyuan Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yuwei Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Yu F, Xie G, Zheng S, Han D, Bao J, Zhang D, Feng B, Wang Q, Zou Q, Wang R, Yang X, Chen W, Lou B, Chen Y. Assessment of the Diagnostic Ability of Four Detection Methods Using Three Sample Types of COVID-19 Patients. Front Cell Infect Microbiol 2021; 11:685640. [PMID: 34164346 PMCID: PMC8216554 DOI: 10.3389/fcimb.2021.685640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/19/2021] [Indexed: 12/18/2022] Open
Abstract
Background Viral nucleic acid detection is considered the gold standard for the diagnosis of coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2 infection. However, unsuitable sample types and laboratory detection kits/methods lead to misdiagnosis, which delays the prevention and control of the pandemic. Methods We compared four nucleic acid detection methods [two kinds of reverse transcription polymerase chain reactions (RT-PCR A: ORF1ab and N testing; RT-PCRB: only ORF1ab testing), reverse transcription recombinase aided amplification (RT-RAA) and droplet digital RT-PCR (dd-RT-PCR)] using 404 samples of 72 hospitalized COVID-19 patients, including oropharyngeal swab (OPS), nasopharyngeal swabs (NPS) and saliva after deep cough, to evaluate the best sample type and method for SARS-CoV-2 detection. Results Among the four methods, dd-RT-PCR exhibited the highest positivity rate (93.0%), followed by RT-PCR B (91.2%) and RT-RAA (91.2%), while the positivity rate of RT-PCR A was only 71.9%. The viral load in OPS [24.90 copies/test (IQR 15.58-129.85)] was significantly lower than that in saliva [292.30 copies/test (IQR 20.20-8628.55)] and NPS [274.40 copies/test (IQR 33.10-2836.45)]. In addition, if OPS samples were tested alone by RT-PCR A, only 21.4% of the COVID-19 patients would be considered positive. The accuracy of all methods reached nearly 100% when saliva and NPS samples from the same patient were tested simultaneously. Conclusions SARS-CoV-2 nucleic acid detection methods should be fully evaluated before use. High-positivity rate methods such as RT-RAA and dd-RT-PCR should be considered when possible. Furthermore, saliva after deep cough and NPS can greatly improve the accuracy of the diagnosis, and testing OPS alone is not recommended.
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Affiliation(s)
- Fei Yu
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Guoliang Xie
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Shufa Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Dongsheng Han
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Jiaqi Bao
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Dan Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Baihuan Feng
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Qi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Qianda Zou
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Ruonan Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Xianzhi Yang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Weizhen Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Bin Lou
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Yu Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China.,Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Zhao N, Jia L, Che J, He X, Zhang B. Novel molecular marker for RAA-LFD visual detection of Cynoglossus semilaevis sex. Anim Reprod Sci 2021; 226:106713. [PMID: 33549888 DOI: 10.1016/j.anireprosci.2021.106713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 11/28/2022]
Abstract
Due to the significant sex dimorphism, Cynoglossus semilaevis has long been a species of research interest in the field of artificial sex manipulation. The existence of pseudo-males both in the natural habitat and aquaculture enterprises also is indicative of the importance for identification of the genetic sex in this species. In the present study, there was elucidation of a novel molecular marker for utilizing the recombinase aided amplification-lateral flow dipstick (RAA-LFD) visual system to identify the genetic sex of C. semilaevis. This 533 bp novel marker is a differential single copy fragment between the Z and W chromosome of C. semilaevis and exists only in the W chromosome. After primer designing and probe labeling, this marker has been utilized in a RAA isothermal amplification system. There were 49 C. semilaevis specimens evaluated for genetic sex identification using both PCR-agarose gel electrophoresis based InDel marker detection and the novel RAA-LFD system. The results from conducting evaluations with the two methods were consistent in all samples. Also, results from sensitivity analysis with use of the RAA-LFD system indicated the detection system was effective and reliable from 108 copy number to 101. With use of the RAA reaction, there was only need to utilize a constant temperature of 37 ℃ for specific DNA amplification within 30 min. The combination use of RAA with LFD resulted in more efficient and convenient sex determination with there being a lesser technical threshold.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Shanghai Ocean University, Shanghai, 201306, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, 300457, China
| | - Jinyuan Che
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, 300457, China
| | - Bo Zhang
- Tianjin Fisheries Research Institute, Tianjin, 300457, China.
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48
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Li F, Ye Q, Chen M, Xiang X, Zhang J, Pang R, Xue L, Wang J, Gu Q, Lei T, Wei X, Ding Y, Wu Q. Cas12aFDet: A CRISPR/Cas12a-based fluorescence platform for sensitive and specific detection of Listeria monocytogenes serotype 4c. Anal Chim Acta 2021; 1151:338248. [PMID: 33608071 DOI: 10.1016/j.aca.2021.338248] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas12a system has displayed remarkable potential in the development of new methods for nucleic acid detection owing to the trans-cleavage activity of Cas12a. Despite the tremendous development in recent years, existing CRISPR/Cas12a-based methods have several limitations such as the time-consuming process, which takes up to 2 h, and the risk of aerosol contamination during DNA amplicon transfer. Herein, we propose a CRISPR/Cas12a-based fluorescence detection platform named "Cas12aFDet" for rapid nucleic acid detection that overcomes these limitations. By integrating PCR or recombinase-aided amplification (RAA) methods with Cas12a-mediated cleavage in a sealed reaction tube, Cas12aFDet-based detection of amplified products could be accomplished within 15 min, while avoiding amplicon contamination. The detection limits of PCR-based Cas12aFDet and RAA-based Cas12aFDet were determined to be 3.37 × 101 cfu/mL and 1.35 × 102 cfu/mL of Listeria monocytogenes serotype 4c in pure culture, respectively. Most importantly, RAA-based Cas12aFDet exhibited 0.64 aM sensitivity for DNA detection, and showed high specificity for detection of other serotypes of Listeria and non-Listeria strains. Furthermore, the feasibility of the RAA-based Cas12aFDet method was evaluated in spiked and natural samples, enabling the quantitative detection of 1.35 × 108-1.35 × 103 cfu/g fresh grass carp of the target L. monocytogenes serotype 4c, and the results obtained for 22 natural aquatic samples were highly consistent with those of the culture-based serotyping method. The established Cas12aFDet platform is expected to provide a new paradigm for the sensitive and specific detection of pathogens in food safety and clinical diagnosis.
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Affiliation(s)
- Fan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinran Xiang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Lei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianhu Wei
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Department of Food Science and Technology, Jinan University, Guangzhou, China.
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.
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49
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Xie G, Zhou D, Zhao G, Feng X, Aguilar ZP, Xu H. Recombinase aided amplification with photoreactive DNA-binding dye for rapid detection of viable Staphylococcus aureus. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110249] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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50
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Zheng YZ, Chen JT, Li J, Wu XJ, Wen JZ, Liu XZ, Lin LY, Liang XY, Huang HY, Zha GC, Yang PK, Li LJ, Zhong TY, Liu L, Cheng WJ, Song XN, Lin M. Reverse Transcription Recombinase-Aided Amplification Assay With Lateral Flow Dipstick Assay for Rapid Detection of 2019 Novel Coronavirus. Front Cell Infect Microbiol 2021; 11:613304. [PMID: 33598439 PMCID: PMC7882697 DOI: 10.3389/fcimb.2021.613304] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/08/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The emerging Coronavirus Disease-2019 (COVID-19) has challenged the public health globally. With the increasing requirement of detection for SARS-CoV-2 outside of the laboratory setting, a rapid and precise Point of Care Test (POCT) is urgently needed. METHODS Targeting the nucleocapsid (N) gene of SARS-CoV-2, specific primers, and probes for reverse transcription recombinase-aided amplification coupled with lateral flow dipstick (RT-RAA/LFD) platform were designed. For specificity evaluation, it was tested with human coronaviruses, human influenza A virus, influenza B viruses, respiratory syncytial virus, and hepatitis B virus, respectively. For sensitivity assay, it was estimated by templates of recombinant plasmid and pseudovirus of SARS-CoV-2 RNA. For clinical assessment, 100 clinical samples (13 positive and 87 negatives for SARS-CoV-2) were tested via quantitative reverse transcription PCR (RT-qPCR) and RT-RAA/LFD, respectively. RESULTS The limit of detection was 1 copies/μl in RT-RAA/LFD assay, which could be conducted within 30 min at 39°C, without any cross-reaction with other human coronaviruses and clinical respiratory pathogens. Compared with RT-qPCR, the established POCT assay offered 100% specificity and 100% sensitivity in the detection of clinical samples. CONCLUSION This work provides a convenient POCT tool for rapid screening, diagnosis, and monitoring of suspected patients in SARS-CoV-2 endemic areas.
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Affiliation(s)
- Yu-Zhong Zheng
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Jiang-Tao Chen
- Department of Medical Laboratory, Huizhou Central People’s Hospital, Huizhou, China
| | - Jian Li
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xian-Jing Wu
- Department of Medical Laboratory, Huizhou Central People’s Hospital, Huizhou, China
| | - Jin-Zhou Wen
- Department of Medical Laboratory, Center for Disease Control and Prevention, Chaozhou, China
| | - Xiang-Zhi Liu
- Department of Medical Laboratory, Chaozhou People’s Hospital, Shantou University Medical College, Chaozhou, China
| | - Li-Yun Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Xue-Yan Liang
- Department of Medical Laboratory, Huizhou Central People’s Hospital, Huizhou, China
- Department of Medical Laboratory, Chaozhou People’s Hospital, Shantou University Medical College, Chaozhou, China
| | - Hui-Ying Huang
- Department of Medical Laboratory, Chaozhou People’s Hospital, Shantou University Medical College, Chaozhou, China
| | - Guang-Cai Zha
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Pei-Kui Yang
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Lie-Jun Li
- Department of Research and Development, Chaozhou Hybribio Limited Corporation, Chaozhou, China
| | - Tian-Yu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Long Liu
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Wei-Jia Cheng
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Xiao-Nan Song
- Department of Human Parasitology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Min Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
- *Correspondence: Min Lin,
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