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Amanzholova M, Shaizadinova A, Bulashev A, Abeldenov S. Genetic identification of Staphylococcus aureus isolates from cultured milk samples of bovine mastitis using isothermal amplification with CRISPR/Cas12a-based molecular assay. Vet Res Commun 2024; 48:291-300. [PMID: 37673833 DOI: 10.1007/s11259-023-10212-z] [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: 07/05/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023]
Abstract
Bovine mastitis, a common and costly disease in dairy cattle, is primarily caused by Staphylococcus aureus. Timely and accurate detection of this pathogen is crucial for effective disease management. In this study, we developed and validated a novel molecular diagnostic assay based on the CRISPR/Cas12a system coupled with Recombinase Polymerase Amplification (RPA) and Loop-Mediated Isothermal Amplification (LAMP). We utilized specific primers targeting the nucleotide sequences of the S.aureus genes of interest, such as nuc and sea. RPA/LAMP reactions were performed under optimized conditions, and the resulting products were subsequently subjected to CRISPR/Cas12a detection. The CRISPR/Cas12a assay successfully detected the target nuc and sea genes, with a limit of detection of 104 and 102 gene copies per reaction, respectively. All 13 S.aureus clinical isolates were identified by RPA-CRISPR/Cas12a assay. The total reaction time is approximately 1 h. The assay demonstrated high sensitivity for the detection of S.aureus in both laboratory and clinical samples.
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Affiliation(s)
- Meruyert Amanzholova
- National Center for Biotechnology, Astana, 010000, Kazakhstan
- L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
| | - Aisha Shaizadinova
- National Center for Biotechnology, Astana, 010000, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aitbay Bulashev
- S. Seifullin Kazakh Agrotechnical Research University, Astana, Kazakhstan
| | - Sailau Abeldenov
- National Center for Biotechnology, Astana, 010000, Kazakhstan.
- S. Seifullin Kazakh Agrotechnical Research University, Astana, Kazakhstan.
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Ma L, Zhu M, Meng Q, Wang Y, Wang X. Real-time detection of Seneca Valley virus by one-tube RPA-CRISPR/Cas12a assay. Front Cell Infect Microbiol 2024; 13:1305222. [PMID: 38259970 PMCID: PMC10800940 DOI: 10.3389/fcimb.2023.1305222] [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: 10/10/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction Senecavirus A (SVA) is a highly contagious virus that causes vesicular disease in pigs. At present, laboratory detection methods, such as virus isolation and polymerase chain reaction (PCR), required precision instruments and qualified personnel, making them unsuitable for point-of-care tests (POCT). Fortunately, the emergence of CRISPR/Cas system has provided new opportunities for fast and efficient pathogen detection. Methods This study successfully developed a precise and sensitive detection platform for diagnosing SVA by combining the CRISPR system with recombinase polymerase amplification (RPA). Results The minimum detection limit of the assay was 10 copies of the SVA genome. Meanwhile, the assay demonstrated high specificity. To validate the effectiveness of this system, we tested 85 swine clinical samples and found that the fluorescence method had a 100% coincidence rate compared to RT-qPCR. Discussion Overall, the RPA-CRISPR/Cas12a assay established in our study is a highly effective method for detecting SVA and holds great potential for practical applications in the resource-limited settings.
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Affiliation(s)
- Lei Ma
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
- College of Life Science, Henan University, Kaifeng, China
| | - Mengjie Zhu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Qingfeng Meng
- Testing Technology R&D Department, Shanghai Kaiwosha Biotechnology Co., Ltd, Shanghai, China
| | - Yao Wang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Xueping Wang
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
- College of Life Science, Henan University, Kaifeng, China
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Zhu Y, Liu J, Liu S, Zhu X, Wu J, Zhou Q, He J, Wang H, Gao W. CRISPR/Cas12a-assisted visible fluorescence for pseudo dual nucleic acid detection based on an integrated chip. Anal Chim Acta 2023; 1280:341860. [PMID: 37858552 DOI: 10.1016/j.aca.2023.341860] [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: 08/23/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND A false negative result is one of the major problems in nucleic acid detection. Failure to screen positive samples for pathogens or viruses poses a risk to public health. This situation will lead to more serious consequences for infectious pathogens or viruses. At present, the common solution is to introduce exogenous or endogenous internal control. Because it amplifies and is detected separately from the target gene, it cannot avoid false negative results caused by DNA extraction failure or reagent inactivation. There is an urgent need for a simple and reliable method to solve the false negative problem of nucleic acid detection. RESULTS We established a chip and an on-chip detection method for the integrated detection of target genes and internal control using the CRISPR system in LAMP amplification products. The chip is processed from a low-cost PMMA board and has three chambers and some channels. After adding the sample, the chip only needs to be rotated twice, and the sample enters three chambers successively depending on its gravity for dual LAMP reaction and CRISPR detections. With a portable LED blue light exciter, visual fluorescence detection is realized. Whether the detection result is positive, negative, or invalid can be determined according to the fluorescence in the CRISPR chamber for target gene and CRISPR chamber for internal control. In this study, the detection of Salmonella enterica in Fenneropenaeus chinensis was taken as an example. The results showed good specificity and sensitivity. It could detect as low as 15 copies/μL of Salmonella enterica. SIGNIFICANCE The on-chip detection solves the problem of aerosol contamination and false negative results. It has the advantages of high sensitivity, high specificity, high accuracy, and low cost. This research will advance the development of nucleic acid detection technology, providing a new and reliable strategy for POCT detection of pathogenic bacteria and viruses.
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Affiliation(s)
- Yuanyuan Zhu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianlin Liu
- Department of Information Technology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
| | - Shanna Liu
- Department of Information Technology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
| | - Xinjian Zhu
- Department of Information Technology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
| | - Qingli Zhou
- Department of Information Technology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China.
| | - Jinsong He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Huanying Wang
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Wenwen Gao
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
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Wang Y, Yang T, Liu G, Xie L, Guo J, Xiong W. Application of CRISPR/Cas12a in the rapid detection of pathogens. Clin Chim Acta 2023; 548:117520. [PMID: 37595863 DOI: 10.1016/j.cca.2023.117520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
The combination of clustered regularly interspaced short palindromic repeats (CRISPR) and its associated Cas protein is an effective gene-editing instrument. Among them, the CRISPR-Cas12a system forms a DNA-cleavage-capable complex with crRNA and exerts its trans-cleavage activity by recognising the PAM site on the target pathogen's gene. After amplifying the pathogenic gene, display materials such as fluorescent probes are added to the detection system, along with the advantages of rapid detection and high sensitivity of the CRISPR system, so that pathogenic bacteria can be diagnosed with greater speed and precision. This article reviews the mechanism of CRISPR-Cas12a in rapid detection, as well as its progress in the rapid detection of pathogenic bacteria in conjunction with various molecular biology techniques, in order to provide a foundation for the future development of a more effective detection platform.
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Affiliation(s)
- Yiheng Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Tianmu Yang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Guifang Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Longfei Xie
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jianying Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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Guo Y, Xia H, Dai T, Liu T. RPA-CRISPR/Cas12a mediated isothermal amplification for visual detection of Phytophthora sojae. Front Cell Infect Microbiol 2023; 13:1208837. [PMID: 37305413 PMCID: PMC10250720 DOI: 10.3389/fcimb.2023.1208837] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/03/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Phytophthora sojae is among the most devastating pathogens of soybean (Glycine max) and severely impacts soybean production in several countries. The resulting disease can be difficult to diagnose and other Phytophthora species can also infect soybean. Accurate diagnosis is important for management of the disease caused by P. sojae. Methods In this study, recombinase polymerase amplification (RPA) in combination with the CRISPR/Cas12a system were used for detection of P. sojae. The assay was highly specific to P. sojae. Results The test results were positive for 29 isolates of P. sojae, but negative for 64 isolates of 29 Phytophthora species, 7 Phytopythium and Pythium species, 32 fungal species, and 2 Bursaphelenchus species. The method was highly sensitive, detecting as little as 10 pg.µL-1 of P. sojae genomic DNA at 37°C in 20 min. The test results were visible under UV light and readout coming from fluorophores. In addition, P. sojae was detected from natural inoculated hypocotyls of soybean seedlings using this novel assay. The rapidity and accuracy of the method were verified using 30 soybean rhizosphere samples. Discussion In conclusion, the RPA-CRISPR/Cas12a detection assay developed here is sensitive, efficient, and convenient, and has potential for further development as a kit for monitoring root rot of soybean in the field.
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Affiliation(s)
- Yufang Guo
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hongming Xia
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingting Dai
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingli Liu
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Xiaozhuang University, Nanjing, China
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