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Li W, Cai B, Chen R, Cui J, Wang H, Li Z. Application of recombinase polymerase amplification with CRISPR/Cas12a and multienzyme isothermal rapid amplification with lateral flow dipstick assay for Bactrocera correcta. PEST MANAGEMENT SCIENCE 2024; 80:3317-3325. [PMID: 38375936 DOI: 10.1002/ps.8035] [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: 09/18/2023] [Revised: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Bactrocera correcta is a quarantine pest that negatively impacts the fruit and vegetable industry. Differentiating B. correcta from similar species, especially in non-adult stages, remains challenging. Rapid molecular identification techniques, such as recombinase polymerase amplification (RPA) combined with CRISPR/Cas12a and multienzyme isothermal rapid amplification with lateral flow dipstick (MIRA-LFD), play a crucial role in early monitoring and safeguarding agricultural production. Our study introduces two methods for the rapid visual identification of B. correcta. RESULTS Bactrocera correcta specific RPA primers, CRISPR RNA (crRNA), and the LFD probe were designed based on the cox1 genes. The RPA reaction conditions were optimized (at 37 °C for 8 min) for effective template DNA amplification. Two nucleic acid detection methods were established to visualize RPA. In the RPA-CRISPR/Cas12a system, the optimal LbCas12a/crRNA concentration ratio was 200:400 nmol L-1. Successful amplification was determined by the presence or absence of green fluorescence following 15 min incubation at 37 °C. The MIRA-LFD system achieved precise identification of the target species within 4 min at 37 °C. Both methods exhibited high specificity and sensitivity, allowing for detection from 1.0 × 10-1 ng μL-1 of DNA. Combined with rapid DNA extraction, rapid identification of individual B. correcta at different developmental stages was achieved, enhancing the practicality and convenience of the established methods. CONCLUSION Our research findings demonstrate that both the RPA-CRISPR/Cas12a and MIRA-LFD methods for B. correcta detection was accurate and rapid (within 30 min and 10 min, respectively), at 37 °C. Our methods do not rely on expensive equipment, thus possess high practical value, providing improved identification solutions for port quarantine pests and field applications. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Weisong Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests of MARA, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, P. R. China
- Sanya Institute of China Agricultural University, Sanya, P. R. China
| | - Bo Cai
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District, Haikou, P. R. China
| | - Ranran Chen
- National Agro-Tech Extension and Service Center, Beijing, P. R. China
| | - Jianchen Cui
- Beijing Plant Protection Station, Beijing, P. R. China
| | - Hui Wang
- Hainan Adminstration of Off-season Plant Breeding, Sanya, P. R. China
| | - Zhihong Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests of MARA, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, P. R. China
- Sanya Institute of China Agricultural University, Sanya, P. R. China
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Sun ML, Yang Y, Hu R, Li JL, Liu SH, Chen YZ, Wang DY, Wang L, Li YZ, Zhong Y, Yao J, Li XN. Simple and field-adapted species identification of biological specimens combining multiplex multienzyme isothermal rapid amplification, lateral flow dipsticks, and universal primers for initial rapid screening without standard PCR laboratory. Int J Legal Med 2024; 138:561-570. [PMID: 37801116 DOI: 10.1007/s00414-023-03101-2] [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: 04/20/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023]
Abstract
Species identification of biological specimens can provide the valuable clues and accelerate the speed of prosecution material processing for forensic investigation, especially when the case scene is inaccessible and the physical evidence is cumbersome. Thus, establishing a rapid, simple, and field-adapted species identification method is crucial for forensic scientists, particularly as first-line technology at the crime scene for initial rapid screening. In this study, we established a new field-adapted species identification method by combining multiplex multienzyme isothermal rapid amplification (MIRA), lateral flow dipstick (LFD) system, and universal primers. Universal primers targeting COX I and COX II genes were used in multiplex MIRA-LFD system for seven species identification, and a dedicated MIRA-LFD system primer targeting CYT B gene was used to detect the human material. DNA extraction was performed by collecting DNA directly from the centrifuged supernatant. Our study found that the entire amplification process took only 15 min at 37 °C and the results of LFDs could be visually observed after 10 min. The detection sensitivity of human material could reach 10 pg, which is equivalent to the detection of single cell. Different common animal samples mixed at the ratio of 1 ng:1 ng, 10 ng:1 ng, and 1 ng:10 ng could be detected successfully. Furthermore, the damaged and degraded samples could also be detected. Therefore, the convenient, feasible, and rapid approach for species identification is suitable for popularization as first-line technology at the crime scene for initial rapid screening and provides a great convenient for forensic application.
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Affiliation(s)
- Mao-Ling Sun
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Ying Yang
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Ran Hu
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jia-Lun Li
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Shu-Han Liu
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Dong-Yi Wang
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Lan Wang
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Yu-Zhang Li
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Yang Zhong
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China.
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China.
| | - Xiao-Na Li
- School of Forensic Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, 110122, People's Republic of China.
- Key Laboratory of Forensic Bio-Evidence Sciences, Liaoning Province, Shenyang, People's Republic of China.
- China Medical University Center of Forensic Investigation, Shenyang, People's Republic of China.
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Yang Z, Wang J, Qi Y, Shi Y, Li F, Wang W, Tian X, Mei X, Zhang Z, Wang S. A novel detection method based on MIRA-CRISPR/Cas13a-LFD targeting the repeated DNA sequence of Trichomonas vaginalis. Parasit Vectors 2024; 17:14. [PMID: 38191422 PMCID: PMC10775430 DOI: 10.1186/s13071-023-06106-3] [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: 10/06/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Trichomonas vaginalis is a protozoan parasite, widely recognized as the most prevalent non-viral sexually transmitted infection (STI) globally. This infection is linked to various complications, including pelvic inflammatory disease, adverse pregnancy outcomes, and an increased risk of acquiring HIV. Current molecular detection methods for T. vaginalis are often costly and technically challenging. METHODS We developed a novel detection method for T. vaginalis using a multi-enzyme isothermal rapid amplification-clustered regularly interspaced short palindromic repeats (MIRA-CRISPR)/Cas13a-lateral flow device (LFD). This assay targets the repeated DNA sequence (GenBank: L23861.1) of T. vaginalis and is performed at a constant temperature of 37 °C for approximately 1 hour. RESULTS The detection limit of genomic DNA (gDNA) using our protocol was 1 × 10-4 ng/μl. Specificity was confirmed by the absence of cross-reaction with gDNA from various other microorganisms such as Staphylococcus aureus, Lactobacillus taiwanensis, Escherichia coli, Monilia albicans, Giardia lamblia, or Toxoplasma gondii. Among 30 clinical samples tested, the positive rates of T. vaginalis detection were 33.33% (10/30) by wet mount microscopy, 40% (12/30) by nested polymerase chain reaction (PCR), 40% (12/30) by MIRA-CRISPR/Cas13a-LFD, and 40% (12/30) by the culture method. Compared with the culture method, the gold standard for diagnosing trichomoniasis, wet mount microscopy showed a sensitivity of 83.3% and moderate diagnostic agreement (kappa value = 0.87). Both nested PCR and MIRA-CRISPR/Cas13a-LFD exhibited 100% sensitivity and excellent diagnostic agreement (kappa value = 1). CONCLUSIONS The MIRA-CRISPR/Cas13a-LFD method is a convenient, rapid, stable, and accurate diagnostic tool for detecting T. vaginalis. This method has the potential to enhance the diagnosis and management of vaginitis, offering a significant improvement over existing diagnostic techniques.
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Affiliation(s)
- Zhenke Yang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Jinghui Wang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Yiming Qi
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Yiping Shi
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Fakun Li
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Weijuan Wang
- Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiaowei Tian
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Xuefang Mei
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Zhenchao Zhang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China.
| | - Shuai Wang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 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: 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: 08/15/2023] [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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Li J, Shang MY, Deng SL, Li M, Su N, Ren XD, Sun XG, Li WM, Li YW, Li RX, Huang Q, Lu WP. Development of a novel integrated isothermal amplification system for detection of bacteria-spiked blood samples. AMB Express 2023; 13:135. [PMID: 38019349 PMCID: PMC10686969 DOI: 10.1186/s13568-023-01643-7] [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: 11/19/2022] [Accepted: 11/19/2023] [Indexed: 11/30/2023] Open
Abstract
Bloodstream infection (BSI) caused by bacteria is highly pathogenic and lethal, and easily develops whole-body inflammatory state. Immediate identification of disease-causing bacteria can improve patient prognosis. Traditional testing methods are not only time-consuming, but such tests are limited to laboratories. Recombinase polymerase amplification combined with lateral flow dipstick (RPA-LFD) holds great promise for rapid nucleic acid detection, but the uncapping operation after amplification easily contaminates laboratories. Therefore, the establishment of a more effective integrated isothermal amplification system has become an urgent problem to be solved. In this study, we designed and fabricated a hermetically sealed integrated isothermal amplification system. Combining with this system, a set of RPA-LFD assays for detecting S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI were established and evaluated. The whole process could be completed in less than 15 min and the results can be visualized by the naked eye. The developed RPA-LFD assays displayed a good sensitivity, and no cross-reactivity was observed in seven similar bacterial genera. The results obtained with 60 clinical samples indicated that the developed RPA-LFD assays had high specifcity and sensitivity for identifying S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI. In conclusion, our results showed that the developed RPA-LFD assay is an alternative to existing PCR-based methods for detection of S. aureus, K. peneumoniae, P. aeruginosa, and H. influenza in BSI in primary hospitals.
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Affiliation(s)
- Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Shao-Li Deng
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Min Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Xian-Ge Sun
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Wen-Man Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Yu-Wei Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Ruo-Xu Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China.
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, P.R. China.
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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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Abu N, Mohd Bakhori N, Shueb RH. Lateral Flow Assay for Hepatitis B Detection: A Review of Current and New Assays. MICROMACHINES 2023; 14:1239. [PMID: 37374824 DOI: 10.3390/mi14061239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
From acute to chronic hepatitis, cirrhosis, and hepatocellular cancer, hepatitis B infection causes a broad spectrum of liver diseases. Molecular and serological tests have been used to diagnose hepatitis B-related illnesses. Due to technology limitations, it is challenging to identify hepatitis B infection cases at an early stage, particularly in a low- and middle-income country with constrained resources. Generally, the gold-standard methods to detect hepatitis B virus (HBV) infection requires dedicated personnel, bulky, expensive equipment and reagents, and long processing times which delay the diagnosis of HBV. Thus, lateral flow assay (LFA), which is inexpensive, straightforward, portable, and operates reliably, has dominated point-of-care diagnostics. LFA consists of four parts: a sample pad where samples are dropped; a conjugate pad where labeled tags and biomarker components are combined; a nitrocellulose membrane with test and control lines for target DNA-probe DNA hybridization or antigen-antibody interaction; and a wicking pad where waste is stored. By modifying the pre-treatment during the sample preparation process or enhancing the signal of the biomarker probes on the membrane pad, the accuracy of the LFA for qualitative and quantitative analysis can be improved. In this review, we assembled the most recent developments in LFA technologies for the progress of hepatitis B infection detection. Prospects for ongoing development in this area are also covered.
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Affiliation(s)
- Norhidayah Abu
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Advanced Materials Research Centre (AMREC), SIRIM Berhad, Lot 34, Jalan Hi-Tech 2/3, Kulim Hi-Tech Park, Kulim 09000, Kedah, Malaysia
| | - Noremylia Mohd Bakhori
- Advanced Materials Research Centre (AMREC), SIRIM Berhad, Lot 34, Jalan Hi-Tech 2/3, Kulim Hi-Tech Park, Kulim 09000, Kedah, Malaysia
| | - Rafidah Hanim Shueb
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
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8
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Hu WW, He JW, Guo SL, Li J. Development and evaluation of a rapid and sensitive multienzyme isothermal rapid amplification with a lateral flow dipstick assay for detection of Acinetobacter baumannii in spiked blood specimens. Front Cell Infect Microbiol 2022; 12:1010201. [PMID: 36339332 PMCID: PMC9626983 DOI: 10.3389/fcimb.2022.1010201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Purpose This study aimed to establish the multienzyme isothermal rapid amplification with a lateral flow dipstick (MIRA-LFD) assay and evaluate its performance in detection of A. baumannii in spiked blood specimens. Methods The study was divided into two stages: a pilot study to establish the methodology and a clinical validation study to evaluate its performance. In the first step, we designed primers specific to detect A. baumannii, optimized the MIRA-LFD assay and analyzed its performance regarding limits of detection, reproducibility, specificity, and efficiency of detection using real-time PCR method. In the second step, we obtained 50 spiked blood isolates and detected these pathogens by MIRA-LFD assay. The MIRA-LFD time was 15 min from DNA sample amplification to complete pathogen detection. Results The developed MIRA-LFD assay displayed a detection limit of 6 CFU/mL for detecting A. baumannii, which was significantly better than that of real-time PCR method, and no cross-reactivity was observed in other non-A. baumannii studied. The results obtained with 50 spiked blood isolates suggested that the developed MIRA-LFD assay had high specificity and sensitivity for identifying A. baumannii. Conclusions This study demonstrates that the established MIRA-LFD assay is time-saving, more effective and sensitive, which may become a powerful tool for rapid and reliable diagnosis of bloodstream infection caused by A. baumannii in primary hospitals.
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Affiliation(s)
- Wei-Wei Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian-Wei He
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Shu-Liang Guo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Jin Li, ; Shu-Liang Guo,
| | - Jin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- *Correspondence: Jin Li, ; Shu-Liang Guo,
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9
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Heng P, Liu J, Song Z, Wu C, Yu X, He Y. Rapid detection of Staphylococcus aureus using a novel multienzyme isothermal rapid amplification technique. Front Microbiol 2022; 13:1027785. [PMID: 36312945 PMCID: PMC9606696 DOI: 10.3389/fmicb.2022.1027785] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
Staphylococcus aureus is a common pathogen that causes various infections. Therefore, it is crucial to develop a fast and easy detection method for diagnosing and preventing S. aureus infections. In this study, MIRA assay was developed and validated (specificity; 100%) for the detection of S. aureus with nuc as the target gene. The reaction temperature and reaction time were then optimized, and the best reaction was at 40°C, 20 min. The assay could detect S. aureus in only 25 min. Additionally, the limit of detection of MIRA was 5 × 102 CFU/ml, 10-fold lower than that of the traditional PCR. Furthermore, this assay efficiently detected 219 S. aureus of 335 strains obtained from different bacterial samples (detection accuracy; 99.40%). In conclusion, this study provides a rapid and easy-to-operate method for the detection of S. aureus, and thus can be used for the timely diagnosis and prevention of S. aureus infection.
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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
| | - Jiakai Liu
- Department of Ultrasound Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan, China
| | - Zhen Song
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Chuan Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xiuzhong Yu
- 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
- *Correspondence: Yang He,
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Liu H, Chang S, Chen S, Du Y, Wang H, Wang C, Xiang Y, Wang Q, Li Z, Wang S, Qiu S, Song H. Highly sensitive and rapid detection of SARS-CoV-2 via a portable CRISPR-Cas13a-based lateral flow assay. J Med Virol 2022; 94:5858-5866. [PMID: 36029033 PMCID: PMC9538558 DOI: 10.1002/jmv.28096] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 01/06/2023]
Abstract
To rapidly identify individuals infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and control the spread of coronavirus disease (COVID-19), there is an urgent need for highly sensitive on-site virus detection methods. A clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas)-based molecular diagnostic method was developed for this purpose. Here, a CRISPR system-mediated lateral flow assay (LFA) for SARS-CoV-2 was established based on multienzyme isothermal rapid amplification, CRISPR-Cas13a nuclease, and LFA. To improve the limit of detection (LoD), the crispr RNA, amplification primer, and probe were screened, in addition to concentrations of various components in the reaction system. The LoD of CRISPR detection was improved to 0.25 copy/μl in both fluorescence- and immunochromatography-based assays. To enhance the quality control of the CRISPR-based LFA method, glyceraldehyde-3-phosphate dehydrogenase was detected as a reference using a triple-line strip design in a lateral flow strip. In total, 52 COVID-19-positive and 101 COVID-19-negative clinical samples examined by reverse transcription polymerase chain reaction (RT-PCR) were tested using the CRISPR immunochromatographic detection technique. Results revealed 100% consistency, indicating the comparable effectiveness of our method to that of RT-PCR. In conclusion, this approach significantly improves the sensitivity and reliability of CRISPR-mediated LFA and provides a crucial tool for on-site detection of SARS-CoV-2.
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Affiliation(s)
- Hongbo Liu
- Chinese PLA Center for Disease Control and PreventionBeijingChina
| | - Shuailei Chang
- Chinese PLA Center for Disease Control and PreventionBeijingChina,Department of Epidemiology, College of Public HealthZhengzhou UniversityZhengzhouChina
| | - Sijia Chen
- Chinese PLA Center for Disease Control and PreventionBeijingChina
| | - Yue Du
- Chinese PLA Center for Disease Control and PreventionBeijingChina,Department of Epidemiology, College of Public HealthZhengzhou UniversityZhengzhouChina
| | - Hui Wang
- Chinese PLA Center for Disease Control and PreventionBeijingChina
| | - Chao Wang
- Chinese PLA Center for Disease Control and PreventionBeijingChina
| | - Ying Xiang
- Chinese PLA Center for Disease Control and PreventionBeijingChina
| | - Qi Wang
- Chinese PLA Center for Disease Control and PreventionBeijingChina
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Shengqi Wang
- Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Shaofu Qiu
- Chinese PLA Center for Disease Control and PreventionBeijingChina
| | - Hongbin Song
- Chinese PLA Center for Disease Control and PreventionBeijingChina
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Development and Evaluation of Duplex MIRA-qPCR Assay for Simultaneous Detection of Staphylococcus aureus and non-aureus Staphylococci. Microorganisms 2022; 10:microorganisms10091734. [PMID: 36144336 PMCID: PMC9502308 DOI: 10.3390/microorganisms10091734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus spp., especially Staphylococcus aureus (S. aureus), is an important pathogen in hospital-acquired infection and food poisoning. Here, we developed a multienzyme isothermal rapid amplification combined with duplex quantitative PCR (duplex MIRA-qPCR) method, which can simultaneously detect the S. aureus species-specific conserved gene FMN-bgsfp and the Staphylococcus genus-specific conserved gene tuf. This assay enabled the amplification of DNA within 20 min at a constant temperature of 39 °C. Specificity analysis indicated that all nine common Staphylococcus species were positive and non-Staphylococcus spp. were negative for tuf gene, whereas S. aureus was positive, non-aureus Staphylococci species and non-Staphylococcus spp. were negative for FMN-bgsfp gene, suggesting that duplex MIRA-qPCR exhibited high specificity. Meanwhile, the sensitivity was tested and the limit of detection (LoD) was 3 × 102 CFU/mL. The coefficient variation values ranged from 0.13% to 2.09%, indicating that the assay had good repeatability. Furthermore, all the nine common Staphylococcus species (including S. aureus) could be detected from four kinds of simulated samples and the LoD of S. aureus was 8.56 × 103 CFU/mL. In conclusion, the duplex MIRA-qPCR has advantages of stronger specificity, lower detection threshold, shorter detection time, and simpler operation, which is an effective tool to detect S. aureus and non-aureus Staphylococci spp. infections rapidly.
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