1
|
Laatri S, El Khayari S, Qriouet Z. Exploring the molecular aspect and updating evolutionary approaches to the DNA polymerase enzymes for biotechnological needs: A comprehensive review. Int J Biol Macromol 2024; 276:133924. [PMID: 39033894 DOI: 10.1016/j.ijbiomac.2024.133924] [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: 03/10/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
DNA polymerases are essential enzymes that play a key role in living organisms, as they participate in the synthesis and maintenance of the DNA molecule. The intrinsic properties of these enzymes have been widely observed and studied to understand their functions, activities, and behavior, which has allowed their natural power in DNA synthesis to be exploited in modern biotechnology, to the point of making them true pillars of the field. In this context, the laboratory evolution of these enzymes, either by directed evolution or rational design, has led to the generation of a wide range of new DNA polymerases with novel properties, suitable for a variety of biotechnological needs. In this review, we examine DNA polymerases at the molecular level, their biotechnological use, and their evolutionary methods in relation to the novel properties sought, providing a chronological selection of evolved DNA polymerases cited in the literature that we consider to be of great interest. To our knowledge, this work is the first to bring together the molecular, functional and evolutionary aspects of the DNA polymerase enzyme. We believe it will be of great interest to researchers whose aim is to produce new lines of evolved DNA polymerases.
Collapse
Affiliation(s)
- Said Laatri
- Microbiology and Molecular Biology Laboratory, Faculty of Sciences, Mohammed V-Souissi University, Rabat 10100, Morocco.
| | | | - Zidane Qriouet
- Pharmacology and Toxicology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V-Souissi University, Rabat 10100, Morocco
| |
Collapse
|
2
|
Liu MH, Guo X, Sun ML, Li JL, Liu SH, Chen YZ, Wang DY, Wang L, Li YZ, Yao J, Li Y, Pan YQ. Rapid detection of human cytomegalovirus by multienzyme isothermal rapid amplification and lateral flow dipsticks. Front Cell Infect Microbiol 2024; 14:1430302. [PMID: 39099883 PMCID: PMC11294213 DOI: 10.3389/fcimb.2024.1430302] [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: 05/09/2024] [Accepted: 07/03/2024] [Indexed: 08/06/2024] Open
Abstract
Introduction Human cytomegalovirus (HCMV) is the most common viral infection seen in newborns. The major route of transmission for acquired human cytomegalovirus infection is breast milk from mothers who are HCMV seropositive to the infants. Thus, a rapid, economical, and simple method to perform HCMV test in breast milk is crucial and necessary for preventing acquired HCMV infection, especially in underdeveloped regions with limited laboratory resources. Methods In this study, an effective technique for the detection of HCMV was constructed by combining multienzyme isothermal rapid amplification (MIRA) and lateral flow chromatography strip (LFD). Primers for the conserved HCMV sequence UL83 were utilized for MIRA-LFD testing. Results Our results showed that the entire MIRA reaction could be completed in 12 minutes at 37°C, and LFD outcomes could be observed visibly after 10 minutes. The detection sensitivity of this method reached 50 copy/μl. Samples of breast milk were examined to compare MIRA-LFD and conventional qPCR. The accuracy of MIRA-LFD was 100%. Discussion The straightforward, rapid, economic features of the test can provide the significant advantages for the prevention of breast milk-acquired cytomegalovirus infection, particularly in resource-limited locations with high seroprevalence of cytomegalovirus.
Collapse
Affiliation(s)
- Ming-hui Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Xiaochong Guo
- Laboratory Animal Center, China Medical University, Shenyang, China
| | - Mao-ling Sun
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jia-lun Li
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Shu-han Liu
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Yun-zhou Chen
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Dong-yi Wang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lan Wang
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Yu-zhang Li
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Yang Li
- Department of Blood Transfusion, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yu-qing Pan
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| |
Collapse
|
3
|
Tu Y, Wang Y, Jiang H, Ren H, Wang X, Lv W. A Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Didymella segeticola Causing Tea Leaf Spot. J Fungi (Basel) 2024; 10:467. [PMID: 39057352 PMCID: PMC11278140 DOI: 10.3390/jof10070467] [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: 06/03/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Tea leaf spot caused by Didymella segeticola is an important disease that threatens the healthy growth of tea plants (Camellia sinensis) and results in reductions in the productivity and quality of tea leaves. Early diagnosis of the disease is particularly important for managing the infection. Loop-mediated isothermal amplification (LAMP) assay is an efficient diagnostic technique with the advantages of simplicity, specificity, and sensitivity. In this study, we developed a rapid, visual, and high-sensitivity LAMP assay for D. segeticola detection based on sequence-characterized amplified regions. Two pairs of amplification primers (external primers F3 and B3 and internal primers FIP and BIP) were designed based on a specific sequence in D. segeticola (NCBI accession number: OR987684). Compared to common pathogens of other genera in tea plants and other species in the Didymella genus (Didymella coffeae-arabicae, Didymella pomorum, and Didymella sinensis), the LAMP method is specific for detecting the species D. segeticola. The assay was able to detect D. segeticola at a minimal concentration of 1 fg/μL genomic DNA at an optimal reaction temperature of 65 °C for 60 min. When healthy leaves were inoculated with D. segeticola in the laboratory, the LAMP method successfully detected D. segeticola in diseased tea leaves at 72 h post inoculation. The LAMP assays were negative when the DNA samples were extracted from healthy leaves. Leaf tissues with necrotic lesions from 18 germplasms of tea plants tested positive for the pathogen by the LAMP assay. In summary, this study established a specific, sensitive, and simple LAMP method to detect D. segeticola, which provides reliable technical support for estimating disease prevalence and facilitates sustainable management of tea leaf spot.
Collapse
Affiliation(s)
- Yiyi Tu
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
| | - Yuchun Wang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Biology, Genetics and breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| | - Hong Jiang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
| | - Hengze Ren
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
| | - Xinchao Wang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Biology, Genetics and breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| | - Wuyun Lv
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Biology, Genetics and breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| |
Collapse
|
4
|
Wang L, Zhang Z, Liu Y, Lin S, Zhang W, Zhu L, Xu W, Dong Y. Allosteric strand displacement isothermal amplification for the visual detection of Toxoplasma gondii in 30 minutes. Biosens Bioelectron 2024; 251:116132. [PMID: 38382270 DOI: 10.1016/j.bios.2024.116132] [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: 12/06/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 02/23/2024]
Abstract
Early detection of Toxoplasma gondii (T. gondii) is critical due to a lack of effective treatment for toxoplasmosis.This study established a simple, cost-effective, and rapid colorimetric detection method for T. gondii. The entire testing process, from sample collection to results, takes only 0.5 h. These characteristics fulfill the demands of researchers seeking rapid target detection with minimal equipment reliance. For genomic extraction, this study evaluated the ability of two filter papers to capture genomes. A rapid genomic extraction device combined with the two filter papers was designed to simplify the genomic extraction process, which was completed within 10 min and increased the detection sensitivity tenfold. The method utilized a simplified primer design for isothermal amplification, namely allosteric strand displacement (ASD), and employed an underutilized commercial color indicator, Bromothymol Blue (BTB), for signal output. Compared with other reported indicators, BTB exhibited a more pronounced color change, shifting from blue to yellow in positive samples, facilitating easier visual differentiation. The reaction was completed in 20 min with a limit of detection (LOD) as low as 0.014 T. gondii per microliter.
Collapse
Affiliation(s)
- Lei Wang
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Zhaoxuan Zhang
- Department of Mechanical Engineering, College of Engineering, China Agricultural University, Beijing, 100083, China
| | - Yanger Liu
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Shenghao Lin
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Wenqiang Zhang
- Department of Mechanical Engineering, College of Engineering, China Agricultural University, Beijing, 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
| | - Yulan Dong
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
5
|
Wang Y, Wang S, Gao Y, Li H, He X, Wang W, Ba Y, Wang L, Jiang J. An approach to rapidly identify the gender of the pigeon by using cross-priming amplification with immune-chromatographic strip. Talanta 2024; 269:125452. [PMID: 38064932 DOI: 10.1016/j.talanta.2023.125452] [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: 03/03/2023] [Revised: 07/20/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Most birds are monomorphic species and breeds, which makes it difficult to determine their gender by appearances, especially the pigeon is a farm animal with economic interest in meat production, ornamentals, sports, and experimental animals. Until now, the available methods for determining the gender of pigeons have mainly consisted of endoscopy, laparoscopy, karyotyping, polymerase chain reaction (PCR), and other similar techniques. Nonetheless, these methods have notable limitations, such as high expenses, invasiveness, and time-consuming procedures, which hinder their practicality for efficiently determining the gender of pigeons. Therefore, an easy, accurate, sensitive, on-site, affordable, and applicable rapid identification of the gender of the pigeon is widely needed for the owner of the pigeon. The purpose of this study was to develop and evaluate the efficacy of Cross-priming amplification (CPA) combined with an immune-chromatographic strip (CPA-strip) for gender identification of the pigeon. The methodology was optimized through various experimental trials. Subsequently, ten samples collected from pigeons were subjected to analysis using the optimized CPA-strip assay, and the results indicated that all female samples were accurately detected. In contrast, the blood samples collected from chickens and ducks were negative when tested with the CPA-strip assay. In conclusion, our study demonstrates the successful establishment of an immune-chromatographic CPA-strip assay for the on-site gender determination of pigeons with high accuracy.
Collapse
Affiliation(s)
- Yimin Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China.
| | - Shan Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Yilin Gao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Hanglin Li
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Xun He
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China
| | - Yierta Ba
- Inner Mongolia Autonomous Region Animal Disease Prevention and Control Center, Tongliao, Inner Mongolia, 028000, PR China
| | - Lei Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China.
| | - Jinqing Jiang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, PR China.
| |
Collapse
|
6
|
Peng L, Fang T, Cai Q, Li H, Li H, Sun H, Zhu M, Dai L, Shao Y, Cai L. Rapid detection of Mycobacterium tuberculosis in sputum using CRISPR-Cas12b combined with cross-priming amplification in a single reaction. J Clin Microbiol 2024; 62:e0092323. [PMID: 38112450 PMCID: PMC10793277 DOI: 10.1128/jcm.00923-23] [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: 07/18/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE In this study, we successfully established a new One-Pot method, named TB One-Pot, for detecting Mtb in sputum by combining CRISPR-cas12b-mediated trans-cleavage with cross-priming amplification (CPA). Our study evaluated the diagnostic performance of TB One-Pot in clinical sputum samples for tuberculosis. The findings provide evidence for the potential of TB One-Pot as a diagnostic tool for tuberculosis.
Collapse
Affiliation(s)
- Lijun Peng
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tingting Fang
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qingshan Cai
- Department of Tuberculosis, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Li
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huanyu Li
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Haiqiong Sun
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mingzhi Zhu
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lingshan Dai
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanqin Shao
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Long Cai
- Clinical Laboratory Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| |
Collapse
|
7
|
Qiao J, Zhao Z, Li Y, Lu M, Man S, Ye S, Zhang Q, Ma L. Recent advances of food safety detection by nucleic acid isothermal amplification integrated with CRISPR/Cas. Crit Rev Food Sci Nutr 2023:1-22. [PMID: 37691410 DOI: 10.1080/10408398.2023.2246558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Food safety problems have become one of the most important public health issues worldwide. Therefore, the development of rapid, effective and robust detection is of great importance. Amongst a range of methods, nucleic acid isothermal amplification (NAIA) plays a great role in food safety detection. However, the widespread application remains limited due to a few shortcomings. CRISPR/Cas system has emerged as a powerful tool in nucleic acid detection, which could be readily integrated with NAIA to improve the detection sensitivity, specificity, adaptability versatility and dependability. However, currently there was a lack of a comprehensive summary regarding the integration of NAIA and CRISPR/Cas in the field of food safety detection. In this review, the recent advances in food safety detection based on CRISPR/Cas-integrated NAIA were comprehensively reviewed. To begin with, the development of NAIA was summarized. Then, the types and working principles of CRISPR/Cas were introduced. The applications of the integration of NAIA and CRISPR/Cas for food safety were mainly introduced and objectively discussed. Lastly, current challenges and future opportunities were proposed. In summary, this technology is expected to become an important approach for food safety detection, leading to a safer and more reliable food industry.
Collapse
Affiliation(s)
- Jiali Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Zhiying Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Yaru Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Minghui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Shengying Ye
- Pharmacy Department, The 983th Hospital of the Joint Logistics Support Force of the, Chinese People's Liberation Army, Tianjin, China
| | - Qiang Zhang
- Branch of Tianjin Third Central Hospital, Tianjin, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| |
Collapse
|
8
|
Wei H, Li J, Liu Y, Cheng W, Huang H, Liang X, Huang W, Lin L, Zheng Y, Chen W, Wang C, Chen W, Xu G, Wei W, Chen L, Zeng Y, Lu Z, Li S, Lin Z, Wang J, Lin M. Rapid and Ultrasensitive Detection of Plasmodium spp. Parasites via the RPA-CRISPR/Cas12a Platform. ACS Infect Dis 2023; 9:1534-1545. [PMID: 37493514 DOI: 10.1021/acsinfecdis.3c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Microscopic examination of thick and thin blood smears stained with Giemsa dye is considered the primary diagnostic tool for the confirmation and management of suspected clinical malaria. However, detecting gametocytes is relatively insensitive, particularly in asymptomatic individuals with low-density Plasmodium infections. To complement existing diagnostic methods, a rapid and ultrasensitive point-of-care testing (POCT) platform for malaria detection is urgently needed and necessary. A platform based on recombinase polymerase amplification (RPA) followed by CRISPR/Cas12a (referred to as RPA-CRISPR/Cas12a) was developed and optimized for the determination of Plasmodium spp. parasites, particularly Plasmodium falciparum, using a fluorescence-based assay (FBDA), lateral flow test strips (LFTS), or naked eye observation (NEO). Then, the established platform was assessed with clinical malaria isolates. Under optimal conditions, the detection threshold was 1 copy/μL for the plasmid, and the limit of detection was 3.11-7.27 parasites/μL for dried blood spots. There was no cross-reactivity against blood-borne pathogens. For the accuracies of RPA-CRISPR/Cas12a, Plasmodium spp. and P. falciparum testing were 98.68 and 94.74%, respectively. The method was consistent with nested PCR results and superior to the qPCR results. RPA-CRISPR/Cas12a is a rapid, ultrasensitive, and reliable platform for malaria diagnosis. The platform requires no or minimal instrumentation for nucleic acid amplification reactions and can be read with the naked eye. Compared with similar diagnostic methods, this platform improves the reaction speed while reducing detection requirements. Therefore, this platform has the potential to become a true POCT for malaria parasites.
Collapse
Affiliation(s)
- Huagui Wei
- Department of Reproductive Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Jian Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Yaqun Liu
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou 521041, People's Republic of China
| | - Weijia Cheng
- Department of Clinical Laboratory, Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan 430081, People's Republic of China
| | - Huiying Huang
- Medical Laboratory of Shenzhen Luohu People's Hospital, Shenzhen 518005, People's Republic of China
| | - Xueyan Liang
- Laboratory Medical Center, Huizhou Municipal Central Hospital, Huizhou 516008, People's Republic of China
| | - Weiyi Huang
- Key Laboratory of Environmental Pollution and Health Risk Assessment, Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Liyun Lin
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou 521041, People's Republic of China
| | - Yuzhong Zheng
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou 521041, People's Republic of China
| | - Weizhong Chen
- Department of Medical Laboratory, Chaozhou People's Hospital Affiliated to Shantou University Medical College, Chaozhou 521011, People's Republic of China
| | - Chunfang Wang
- Department of Reproductive Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Wencheng Chen
- Guangxi Medical and Health Key Discipline Construction Project of the Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Guidan Xu
- Department of Reproductive Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Wujun Wei
- Department of Reproductive Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Liying Chen
- Industrial College of Biomedicine and Health Industry, Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Yongmei Zeng
- Department of Medical Laboratory, Chaozhou People's Hospital Affiliated to Shantou University Medical College, Chaozhou 521011, People's Republic of China
| | - Zefang Lu
- Department of Medical Laboratory, Chaozhou People's Hospital Affiliated to Shantou University Medical College, Chaozhou 521011, People's Republic of China
| | - Shujuan Li
- School of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou 521041, People's Republic of China
| | - Zongyun Lin
- Department of Reproductive Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Junli Wang
- Department of Reproductive Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
- Key Laboratory of Environmental Pollution and Health Risk Assessment, Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
- Reproductive Medicine, Guangxi Medical and Health Key Discipline Construction Project, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| | - Min Lin
- Department of Reproductive Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, People's Republic of China
| |
Collapse
|
9
|
Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
Collapse
Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
| |
Collapse
|
10
|
Mao R, Wu X, Miao Q, Cai T. Asymmetric stem-loop–mediated isothermal amplification of nucleic acids for DNA diagnostic assays by simple modification of canonical PCR primers. Front Bioeng Biotechnol 2022; 10:931770. [PMID: 35935482 PMCID: PMC9355699 DOI: 10.3389/fbioe.2022.931770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Nucleic acid–based assays have been adopted as mainstream tools for clinical diagnostics, food safety, and environment monitoring with the merits of accuracy, rapidity, and sensitivity. Loop-mediated isothermal amplification (LAMP) is a well-established method to rapidly identify nucleic acids and has gained recognition and been developed for clinical applications in resource-limited areas. However, the needs for specifically designed primer sets and non-specific amplification hinder the development of LAMP-based nucleic acid tests. Here, a promoted method, termed asymmetric stem-loop–mediated isothermal amplification (ASLAMP) by simple modification of canonical PCR primers, was developed to attempt to overcome those drawbacks. The two primers in the ASLAMP reaction can be easily obtained by adding a stem-loop sequence part to one PCR primer at 5′-ends to get the folding primer (FP), then adding the same primer to the counter canonical PCR primer at 5′-ends to get the turn-back primer (TP). The ASLAMP method was demonstrated in detecting the H1N1 gene fragment with merits of simple primer design, short target sequence, and high amplification efficiency. In addition, the ASLAMP method showed similar efficacy compared with LAMP targeting at the same H1N1 gene sequence. Furthermore, Shigella detection monitored by real-time fluorescence and endpoint colorimetric approaches were taken as examples for evaluation of the practical application of the ASLAMP method, both offered 100% sensitivity and specificity. In conclusion, the novel ASLAMP method with simplicity of primer design, low requirement of equipment, efficiency, and rapidity has exhibited its great prospect for establishment of DNA isothermal amplification in point of care application.
Collapse
Affiliation(s)
- Rui Mao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- *Correspondence: Rui Mao, ; Ting Cai,
| | - Xinyao Wu
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Qing Miao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Ting Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- *Correspondence: Rui Mao, ; Ting Cai,
| |
Collapse
|
11
|
Sereno D, Oury B, Geiger A, Vela A, Karmaoui A, Desquesnes M. Isothermal Nucleic Acid Amplification to Detect Infection Caused by Parasites of the Trypanosomatidae Family: A Literature Review and Opinion on the Laboratory to Field Applicability. Int J Mol Sci 2022; 23:7543. [PMID: 35886895 PMCID: PMC9322063 DOI: 10.3390/ijms23147543] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 12/13/2022] Open
Abstract
Isothermal amplification of nucleic acids has the potential to be applied in resource-limited areas for the detection of infectious agents, as it does not require complex nucleic purification steps or specific and expensive equipment and reagents to perform the reaction and read the result. Since human and animal infections by pathogens of the Tryponasomatidae family occur mainly in resource-limited areas with scant health infrastructures and personnel, detecting infections by these methodologies would hold great promise. Here, we conduct a narrative review of the literature on the application of isothermal nucleic acid amplification for Trypanosoma and Leishmania infections, which are a scourge for human health and food security. We highlight gaps and propose ways to improve them to translate these powerful technologies into real-world field applications for neglected human and animal diseases caused by Trypanosomatidae.
Collapse
Affiliation(s)
- Denis Sereno
- Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, Parasite Infectiology and Public Health Group, 34032 Montpellier, France
| | - Bruno Oury
- Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, CIRAD, Parasite Infectiology and Public Health Group, 34032 Montpellier, France
| | - Anne Geiger
- Centre International de Recherche en Agronomie pour le Développement, Institut de Recherche pour le Développement, Université de Montpellier, UMR INTERTRYP IRD, 34032 Montpellier, France
| | - Andrea Vela
- One Health Research Group, Facultad de Ciencias de la Salud, Universidad de las Américas-Quito, Calle de los Colimes y Avenida De los Granados, Quito 170513, Ecuador
| | - Ahmed Karmaoui
- Bioactives (Health and Environmental, Epigenetics Team), Faculty of Sciences and Techniques, Errachidia (UMI), Moroccan Center for Culture and Sciences, University Moulay Ismail, Meknes 50000, Morocco
| | - Marc Desquesnes
- CIRAD, UMR INTERTRYP, 31076 Toulouse, France
- INTERTRYP, Université de Montpellier, CIRAD, IRD, 34032 Montpellier, France
| |
Collapse
|
12
|
Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
Collapse
|
13
|
Chen G, Yu J, Chen H, Cen K, Zhou Y, You Q, Wu S. EasyNAT MP Assay: A Simple, Rapid, and Low-Cost Method to Detect Mycoplasma pneumoniae Using Cross-Priming Amplification Technology. Mol Diagn Ther 2022; 26:345-352. [PMID: 35430704 PMCID: PMC9098574 DOI: 10.1007/s40291-022-00582-6] [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] [Accepted: 03/09/2022] [Indexed: 11/29/2022]
Abstract
Background Mycoplasma pneumoniae (MP) is the most common pathogen of atypical pneumonia and the main cause of community-acquired pneumonia (CAP) in infants and older adults. This study aimed at investigating a method based on the cross-priming amplification (CPA) technique for the rapid detection of MP in clinical specimens collected from patients with CAP. Methods The sensitivity and specificity of the EasyNAT MP assay were determined. Oropharyngeal swab specimens were collected from 162 in-patients of Hangzhou First People’s Hospitals from January 2018 to December 2020. The patients were aged between 1 and 15 years with symptoms, signs, and chest radiographs consistent with CAP. This study evaluated the presence of MP in the clinical specimens using the EasyNAT method and the conventional fluorescence quantitative PCR technique. Results The limit of detection using the EasyNAT MP assay was 500 copies/mL, while the test results of the other 13 common pathogens causing CAP or colonizing in the upper respiratory tract showed no cross-reactivity. Of 162 specimens, EasyNAT MP gave a positive indication in 82 specimens. Compared with conventional fluorescence quantitative PCR, the positive coincidence rate and the negative coincidence rate of EasyNAT MP was found to be 100.00% and 97.56%, respectively. Of the 82 specimens, two specimens were determined to be negative by the conventional fluorescence quantitative PCR, but were positive for EasyNAT MP. The two samples were re-extracted and confirmed to be positive by conventional fluorescence quantitative PCR. Conclusion EasyNAT MP is suitable as an initial test for MP diagnosis due to its simplicity, low turnaround time, and high sensitivity and specificity.
Collapse
Affiliation(s)
- Guang Chen
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310012, Zhejiang, People's Republic of China
| | - Junwei Yu
- Ustar Biotechnologies (Hangzhou) Ltd., Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Hanlu Chen
- The Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310000, Zhejiang, People's Republic of China
| | - Ke Cen
- Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Yanqiong Zhou
- Ustar Biotechnologies (Hangzhou) Ltd., Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Qimin You
- Ustar Biotechnologies (Hangzhou) Ltd., Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Shenghai Wu
- The Fourth Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310000, Zhejiang, People's Republic of China. .,Department of Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, People's Republic of China.
| |
Collapse
|
14
|
Mota DS, Guimarães JM, Gandarilla AMD, Filho JCBS, Brito WR, Mariúba LAM. Recombinase polymerase amplification in the molecular diagnosis of microbiological targets and its applications. Can J Microbiol 2022; 68:383-402. [PMID: 35394399 DOI: 10.1139/cjm-2021-0329] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since the introduction of the polymerase chain reaction (PCR) technique in 1983, nucleic acid amplification has permeated all fields of biological science, particularly clinical research. Despite its importance, PCR has been restricted to specialized centers and its use in laboratories with few resources is limited. In recent decades, there has been a notable increase in the development of new isothermal technologies for molecular diagnosis with the hope of overcoming the traditional limitations of the laboratory. Among these technologies, recombinase polymerase amplification (RPA) has a wide application potential because it does not require thermocyclers and has high sensitivity, specificity, simplicity, and detection speed. This technique has been used for DNA and RNA amplification in various pathogenic organisms such as viruses, bacteria, and parasites. In addition, RPA has been successfully implemented in different detection strategies, making it a promising alternative for performing diagnoses in environments with scarce resources and a high burden of infectious diseases. In this study, we present a review of the use of RPA in clinical settings and its implementation in various research areas.
Collapse
Affiliation(s)
- D S Mota
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J M Guimarães
- Centro Multiusuário para Análises de Fenômenos Biomédicos, Universidade do Estado do Amazonas (UEA), Manaus, AM, 69065-00, Brazil
| | - A M D Gandarilla
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - J C B S Filho
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - W R Brito
- Departamento de Química, ICE, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Laboratório de Bioeletrônica e Eletroquímica, LABEL, Central Analítica, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil
| | - L A M Mariúba
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biotecnologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, 69057-070, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| |
Collapse
|
15
|
Automatic system for high-throughput and high-sensitivity diagnosis of SARS-CoV-2. Bioprocess Biosyst Eng 2022; 45:503-514. [PMID: 35031864 PMCID: PMC8760113 DOI: 10.1007/s00449-021-02674-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/27/2021] [Indexed: 11/13/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had severe consequences for health and the global economy. To control the transmission, there is an urgent demand for early diagnosis and treatment in the general population. In the present study, an automatic system for SARS-CoV-2 diagnosis is designed and built to deliver high specification, high sensitivity, and high throughput with minimal workforce involvement. The system, set up with cross-priming amplification (CPA) rather than conventional reverse transcription-polymerase chain reaction (RT-PCR), was evaluated using more than 1000 real-world samples for direct comparison. This fully automated robotic system performed SARS‐CoV‐2 nucleic acid-based diagnosis with 192 samples in under 180 min at 100 copies per reaction in a “specimen in data out” manner. This throughput translates to a daily screening capacity of 800–1000 in an assembly-line manner with limited workforce involvement. The sensitivity of this device could be further improved using a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based assay, which opens the door to mixed samples, potentially include SARS-CoV-2 variants screening in extensively scaled testing for fighting COVID-19.
Collapse
|
16
|
Yang QQ, Zhao XX, Wang D, Zhang PJ, Hu XN, Wei S, Liu JY, Ye ZH, Yu XP. A reverse transcription-cross-priming amplification method with lateral flow dipstick assay for the rapid detection of Bean pod mottle virus. Sci Rep 2022; 12:681. [PMID: 35027575 PMCID: PMC8758742 DOI: 10.1038/s41598-021-03562-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
Bean pod mottle virus (BPMV) is a destructive virus that causes serious economic losses in many countries every year, highlighting the importance of its effective detection. In this study, we developed a fast reverse transcription-cross-priming amplification (RT-CPA) coupled with lateral flow dipstick (LFD) diagnostic method for BPMV detection. The RT-CPA-LFD assay that targets the coat protein gene of BPMV was highly specific against diagnosing four other common viruses transmitted by soybean seeds, i.e., Southern bean mosaic virus (SBMV), Tomato ringspot virus (ToRSV), Arabis mosaic virus (ArMV), and Tobacco ringspot virus (TRSV). The sensitivities of the real-time fluorescent RT-CPA and the RT-CPA-LFD assay were at least 50 pg/μl and 500 pg/μl, respectively. Despite a compromise in the limit of detection of the RT-CPA method compared with TaqMan-MGB real-time RT-PCR, our results demonstrated a notably better performance in the detection of field samples of BPMV-infested soybean seeds. With the advantages of efficiency and convenience by visual determination, the RT-CPA-LFD assay presents a potential application for the rapid and accurate detection of BPMV in routine tests.
Collapse
Affiliation(s)
- Qian-Qian Yang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China.
| | - Xing-Xing Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Dao Wang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Peng-Jun Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xue-Nan Hu
- Guangzhou Customs Technology Center, Guangzhou, China
| | - Shuang Wei
- Guangzhou Customs Technology Center, Guangzhou, China
| | | | - Zi-Hong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiao-Ping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China.
| |
Collapse
|
17
|
Sun ML, Lai HY, Chong NY, Liu DF, Zhang ZY, Pang B, Yao J. Simple and Feasible Detection of Hepatitis B Virus via Combination of Multienzyme Isothermal Rapid Amplification and Lateral Flow Dipstick Strip. Front Mol Biosci 2021; 8:763079. [PMID: 34926579 PMCID: PMC8674754 DOI: 10.3389/fmolb.2021.763079] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/08/2021] [Indexed: 12/04/2022] Open
Abstract
Hepatitis B virus infection is not only a huge burden in the field of social health but also a major public health problem that affects the lives and health of the people. Simple, rapid, feasible detection of HBV is critical for its prevention and spread, especially in the developing countries with low-resource laboratories. To this end, we combined multienzyme isothermal rapid amplification (MIRA) and lateral flow dipstick (LFD) strip to detect HBV. A pair of primers targeting the conserved region of HBV genome was designed and used in MIRA-LFD assay. Our results found that the entire amplification of MIRA-LFD only takes 10 min at 37°C and the dilution of the amplification products was added in the LFD strip and observed by the naked eye after 10 min. The detection sensitivity of this method can reach 10 pg. The 45 clinical samples were detected by MIRA-LFD and real-time PCR. The accuracy rate of MIRA-LFD was 100%. Therefore, these characteristics of our newly developed MIRA-LFD assay make it particularly useful and suitable for detecting HBV in the resource-limited condition.
Collapse
Affiliation(s)
- Mao-Ling Sun
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Hai-Yun Lai
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Na-Yu Chong
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Dong-Fan Liu
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Zhen-Yi Zhang
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Bo Pang
- School of Forensic Medicine, China Medical University, Shenyang, China
| | - Jun Yao
- School of Forensic Medicine, China Medical University, Shenyang, China
| |
Collapse
|
18
|
Banerjee S, Biswas SK, Kedia N, Sarkar R, De A, Mitra S, Roy S, Chowdhury R, Samaddar S, Bandopadhyay A, Banerjee I, Jana S, Goswami R, Dutta S, Chawla-Sarkar M, Chakraborty S, Mondal A. Piecewise Isothermal Nucleic Acid Testing (PINAT) for Infectious Disease Detection with Sample-to-Result Integration at the Point-of-Care. ACS Sens 2021; 6:3753-3764. [PMID: 34582171 DOI: 10.1021/acssensors.1c01573] [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] [Indexed: 11/30/2022]
Abstract
We developed a piecewise isothermal nucleic acid test (PINAT) as a platform technology for diagnosing pathogen-associated infections, empowered by an illustrative novel methodology that embeds an exclusive DNA-mediated specific probing reaction with the backbone of an isothermal reverse transcription cum amplification protocol for detecting viral RNA. In a point-of-care format, this test is executable in a unified single-step, single-chamber procedure, leading to seamless sample-to-result integration in an inexpensive, scalable, pre-programmable, and customizable portable device, with mobile-app-integrated interpretation and analytics involving minimal manually operative procedures. The test exhibited a high sensitivity and specificity of detection when assessed using 200 double-blind patient samples for detecting SARS-CoV-2 infection by the Indian Council of Medical Research (ICMR), and subsequently using 170 double-blind patient samples in a point-of-care format outside controlled laboratory settings as performed by unskilled technicians in an organized clinical trial. We also established its efficacy in detecting Influenza A infection by performing the diagnosis at the point of collection with uncompromised detection rigor. The envisaged trade-off between advanced laboratory-based molecular diagnostic procedures and the elegance of common rapid tests renders the method ideal for deployment in resource-limited settings towards catering the needs of the underserved.
Collapse
Affiliation(s)
- Saptarshi Banerjee
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Sujay Kumar Biswas
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur 721302, India
| | - Nandita Kedia
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Rakesh Sarkar
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Aratrika De
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Suvrotoa Mitra
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Subhanita Roy
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | - Ranjini Chowdhury
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | | | - Aditya Bandopadhyay
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | - Indranath Banerjee
- B.C. Roy Technology Hospital, Indian Institute of Technology, Kharagpur 721302, India
| | - Subhasis Jana
- Purba Medinipur District Hospital, Tamluk, Purba Medinipur, West Bengal 721636, India
| | - Ritobrata Goswami
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Mamta Chawla-Sarkar
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata 700010, India
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur 721302, India
| | - Arindam Mondal
- School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India
| |
Collapse
|
19
|
Huang J, Xiao Z, Yang X, Chen X, Wang X, Chen Y, Zheng W, Chen W, Chen H, Li S. Two target genes based multiple cross displacement amplification combined with a lateral flow biosensor for the detection of Mycobacterium tuberculosis complex. BMC Microbiol 2021; 21:267. [PMID: 34607556 PMCID: PMC8491432 DOI: 10.1186/s12866-021-02328-6] [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: 12/07/2020] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Background Tuberculosis (TB) is a serious chronic infectious disease caused by Mycobacterium tuberculosis complex (MTBC). Hence, the development of a novel, simple, rapid and sensitive method to detect MTBC is of great significance for the prevention and treatment of TB. Results In this study, multiple cross displacement amplification (MCDA) combined with a nanoparticle-based lateral flow biosensor (LFB) was developed to simultaneously detect two target genes (IS6110 and mpb64) of MTBC (MCDA-LFB). One suite of specific MCDA primers designed for the IS6110 and mpb64 genes was validated using genomic DNA extracted from the reference strain H37Rv. The MCDA amplicons were analyzed using a real-time turbidimeter, colorimetric indicator (malachite green, MG) and LFBs. The optimal amplification temperature and time were confirmed, and the MCDA-LFB method established in the current report was evaluated by detecting various pathogens (i.e., reference strains, isolates and clinical sputum samples). The results showed that the two sets of MCDA primers targeting the IS6110 and mpb64 genes could effectively detect MTBC strains. The optimal reaction conditions for the MCDA assay were determined to be 67 °C for 35 min. The MCDA assay limit of detection (LoD) was 100 fg per reaction for pure genomic DNA. The specificity of the MCDA-LFB assay was 100%, and there were no cross-reactions for non-MTBC strains. For sputum samples and MTBC strain detection, the positive rate of MCDA-LFB for the detection of MTBC strains was consistent with seminested automatic real-time PCR (Xpert MTB/RIF) and higher than acid-fast staining (AFS) and culture assays when used for sputum samples. The MCDA-LFB assay was a rapid tool, and the whole procedure for MCDA-LFB, including DNA template preparation, MCDA reaction and amplification product analysis, was completed within 70 min. Conclusion The MCDA-LFB assay targeting the IS6110 and mpb64 genes is a simple, rapid, sensitive and reliable detection method, and it has potential significance for the prevention and treatment of TB.
Collapse
Affiliation(s)
- Junfei Huang
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China
| | - Ziyu Xiao
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China.,Public Health School, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Xinggui Yang
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China.,Public Health School, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Xu Chen
- The Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, People's Republic of China
| | - Xiaojuan Wang
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China.,Public Health School, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Yijiang Chen
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China
| | - Wenlin Zheng
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China
| | - Wei Chen
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China
| | - Huijuan Chen
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China
| | - Shijun Li
- Laboratory of Infectious Disease of Experimental Center, Guizhou Provincial Center for Disease Control and Prevention, 73 Bageyan Road, Guiyang, 550004, Guizhou, People's Republic of China. .,Public Health School, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China.
| |
Collapse
|
20
|
Prasitporn T, Senapin S, Vaniksampanna A, Longyant S, Chaivisuthangkura P. Development of cross-priming amplification (CPA) combined with colorimetric and lateral flow dipstick visualization for scale drop disease virus (SDDV) detection. JOURNAL OF FISH DISEASES 2021; 44:1411-1422. [PMID: 34041757 DOI: 10.1111/jfd.13448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Scale drop disease virus (SDDV) is one of the most important pathogens that causes scale drop disease (SDD) in Asian sea bass (Lates calcarifer). The outbreaks of this disease are one of the factors causing substantial losses in Asian sea bass aquaculture. In this study, the uracil-DNA glycosylase (UDG)-supplemented cross-priming amplification (UCPA) combined with a colorimetric detection method using the hydroxynaphthol blue (HNB) and lateral flow dipstick (LFD) for detection of SDDV was developed. The UDG was utilized to prevent carryover contamination, and the CPA reactions can be readily observed by HNB and LFD. The CPA primers and probe were designed to target the major capsid protein (MCP) gene of the SDDV. The optimized UCPA conditions were performed at the temperature of 61°C for 60 min. The UCPA assays demonstrated specificity to SDDV without cross-reaction to other tested viruses including red-spotted grouper nervous necrosis virus (RGNNV), infectious spleen and kidney necrosis virus (ISKNV) and Lates calcarifer herpes virus (LCHV), and other bacterial species commonly found in aquatic animals. The sensitivity of the UCPA-HNB and UCPA-LFD was 100 viral copies/µl and 10 pg of extracted total DNA, which was 10-fold more sensitive than that of conventional PCR. The UCPA-HNB and UCPA-LFD assays could be used to detect the SDDV infection in all 25 confirmed SDDV-infected fish samples. Therefore, the UCPA coupled with HNB and LFD was rapid, simple and effective and might be applied for diagnosis of SDDV infection.
Collapse
Affiliation(s)
- Terawut Prasitporn
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
| | - Saengchan Senapin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | - Siwaporn Longyant
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
| | - Parin Chaivisuthangkura
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand
- Center of Excellence in Animal, Plant and Parasite Biotechnology, Srinakharinwirot University, Bangkok, Thailand
| |
Collapse
|
21
|
Zhang Z, Du J, Liu T, Wang F, Jia J, Dong L, Zhao L, Xue Y, Jiang G, Yu X, Huang H. EasyNAT MTC assay: A simple, rapid, and low-cost cross-priming amplification method for the detection of mycobacterium tuberculosis suitable for point-of-care testing. Emerg Microbes Infect 2021; 10:1530-1535. [PMID: 34288833 PMCID: PMC8330774 DOI: 10.1080/22221751.2021.1959271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
More sensitive, rapid, and affordable diagnostic tools for pulmonary tuberculosis (PTB) are urgently needed. This study aimed to assess the performance of EasyNAT MTC (abbreviation: EasyNAT) (Ustar Biotechnologies, China), a novel isothermal amplification method with a turnaround time of less than two hours that requires a few manual steps to process the sputum. Sputum samples from 249 patients with suspected PTB were subjected to smear, culture, Xpert MTB/RIF (Cepheid, USA) and EasyNAT assay testing. Of the 169 PTB patients, EasyNAT detected more PTB patients than Xpert (72.19% vs. 61.54%, P < 0.05, χ2 = 4.326). Both the Xpert assay and EasyNAT assay detected almost all the culture-positive sputa successfully, but EasyNAT yielded more positive results among the smear-negative and culture-negative PTB cases (44.59% (33/74) vs. 22.97% (17/74), P < 0.01, χ2 = 7.732). Although the specificity of EasyNAT was lower in contrast to Xpert [95.00% (76/80) vs. 98.75% (79/80)], the difference was not significant (P = 0.363, χ2 = 0.826). EasyNAT could be used as an initial test for PTB diagnosis due to its simplicity, rapid turnaround time, high sensitivity, and low cost.
Collapse
Affiliation(s)
- Zhuman Zhang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Jian Du
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Tao Liu
- Department of Anesthesiology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Fen Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Junnan Jia
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Lingling Dong
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Liping Zhao
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Yi Xue
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| |
Collapse
|
22
|
Glökler J, Lim TS, Ida J, Frohme M. Isothermal amplifications - a comprehensive review on current methods. Crit Rev Biochem Mol Biol 2021; 56:543-586. [PMID: 34263688 DOI: 10.1080/10409238.2021.1937927] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
Collapse
Affiliation(s)
- Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Jeunice Ida
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Marcus Frohme
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| |
Collapse
|
23
|
Zhang D, Liu D, Liu B, Ma X. Development of a Novel Multiple Cross-Linking Spiral Amplification for Rapid and Sensitive Detection of HPV16 DNA. J Microbiol Biotechnol 2021; 31:610-620. [PMID: 33526756 PMCID: PMC9705923 DOI: 10.4014/jmb.2012.12047] [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: 12/27/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
PCRThere has been increasing interest in the head and neck squamous cell carcinoma (HNSCC) that is caused by high-risk human papillomavirus (HR-HPV) and has posed a significant challenge to Otolaryngologists. A rapid, sensitive, and reliable method is required for the detection of HR-HPV in clinical specimens to prevent and treat HPV-induced diseases. In this study, a multiple cross-linking spiral amplification (MCLSA) assay was developed for the visual detection of HPV-16. In the MCLSA assay, samples were incubated under optimized conditions at 62°C for 45 min, and after mixing with the SYBR Green I (SGI) dye, the positive amplicons showed bright green fluorescence while the negative amplicons exhibited no obvious change. The specificity test revealed that the developed MCLSA technique had high specificity and could effectively distinguish all five HPV-16 strains from other pathogenic microorganisms. In terms of analytical sensitivity, the limit of detection (LoD) of MCLSA assay was approximately 5.4 × 101 copies/tube, which was 10-fold more sensitive than loop-mediated isothermal amplification (LAMP) and RT-PCR. The detection results of laryngeal cancer specimens collected from 46 patients with suspected HPV infection in the Liaoning region demonstrated that the positive detection rates of MCLSA and hybridized capture 2 kit were 32.61% (15/46). The true positive rate of the MCLSA assay was higher than that of RT-PCR (100% vs. 93.33%) and LAMP (100% vs. 86.67%). Therefore, the MCLSA assay developed in the present study could be a potentially useful tool for the point-of-care (PoC) diagnosis of HR-HPV, especially in resource-limited countries.
Collapse
Affiliation(s)
- Donghong Zhang
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, P.R. China
| | - Dongliang Liu
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, P.R. China
| | - Bing Liu
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, P.R. China
| | - Xiulan Ma
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, P.R. China,Corresponding author Phone/Fax: +86-15004064649 E-mail:
| |
Collapse
|
24
|
Wang J, Gao S, Yang J, Liu J, Li Y, Luo J, Guan G, Yin H. Cross-priming amplification targeting the 18S rRNA gene for the rapid diagnosis of Babesia bovis infection. Ticks Tick Borne Dis 2021; 12:101713. [PMID: 33827035 DOI: 10.1016/j.ttbdis.2021.101713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/25/2022]
Abstract
Babesia bovis is a known causative agent of bovine babesiosis and is widely distributed across China. Rapid detection and accurate identification of B. bovis is essential for follow-up management and epidemiological investigations. In this study, a cross-priming amplification combined with vertical flow (CPA-VF) assay was developed. The detection limit of the CPA-VF assay targeting the 18S rRNA gene was 320 fg per reaction at 61 °C for 60 min. No cross-reactions were observed with other piroplasms infective to cattle. Furthermore, 36 blood samples from experimentally-infected animals were accurately assessed using the CPA-VF assay. The performance of the CPA-VF assay was compared with the results of conventional PCR for 219 blood samples from the field. Our results demonstrate that the CPA-VF assay is a practical and effective diagnostic tool for bovine babesiosis caused by B. bovis infection.
Collapse
Affiliation(s)
- Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
| | - Shandian Gao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
| | - Jifei Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, PR China.
| |
Collapse
|
25
|
Kumar Y. Isothermal amplification-based methods for assessment of microbiological safety and authenticity of meat and meat products. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107679] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
26
|
Jiang H, Wang K, Yan M, Ye Q, Lin X, Chen L, Ye Y, Zhang L, Liu J, Huang T. Pathogenic and Virulence Factor Detection on Viable but Non-culturable Methicillin-Resistant Staphylococcus aureus. Front Microbiol 2021; 12:630053. [PMID: 33841357 PMCID: PMC8027501 DOI: 10.3389/fmicb.2021.630053] [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: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 02/05/2023] Open
Abstract
Food safety and foodborne infections and diseases have been a leading hotspot in public health, and methicillin-resistant Staphylococcus aureus (MRSA) has been recently documented to be an important foodborne pathogen, in addition to its recognition to be a leading clinical pathogen for some decades. Standard identification for MRSA has been commonly performed in both clinical settings and food routine detection; however, most of such so-called "standards," "guidelines," or "gold standards" are incapable of detecting viable but non-culturable (VBNC) cells. In this study, two major types of staphylococcal food poisoning (SFP), staphylococcal enterotoxins A (sea) and staphylococcal enterotoxins B (seb), as well as the panton-valentine leucocidin (pvl) genes, were selected to develop a cross-priming amplification (CPA) method. Limit of detection (LOD) of CPA for sea, seb, and pvl was 75, 107.5, and 85 ng/μl, indicating that the analytical sensitivity of CPA is significantly higher than that of conventional PCR. In addition, a rapid VBNC cells detection method, designated as PMA-CPA, was developed and further applied. PMA-CPA showed significant advantages when compared with PCR assays, in terms of rapidity, sensitivity, specificity, and accuracy. Compared with conventional VBNC confirmation methods, the PMA-CPA showed 100% accordance, which had demonstrated that the PMA-CPA assays were capable of detecting different toxins in MRSA in VBNC state. In conclusion, three CPA assays were developed on three important toxins for MRSA, and in combination with PMA, the PMA-CPA assay was capable of detecting virulent gene expression in MRSA in the VBNC state. Also, the above assays were further applied to real samples. As concluded, the PMA-CPA assay developed in this study was capable of detecting MRSA toxins in the VBNC state, representing first time the detection of toxins in the VBNC state.
Collapse
Affiliation(s)
- Hua Jiang
- Department of Haematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Kan Wang
- Center for Translational Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Muxia Yan
- Department of Haematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qian Ye
- Department of Haematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaojing Lin
- Department of Haematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ling Chen
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, China
| | - Yanrui Ye
- School of Biological Science and Engineering, South China University of Technology, Guangzhou, China
| | - Li Zhang
- Department of Haematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Junyan Liu
- Department of Civil and Environmental Engineering, University of Maryland, College Park, College Park, MD, United States
- *Correspondence: Junyan Liu,
| | - Tengyi Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
- Tengyi Huang,
| |
Collapse
|
27
|
Kumar Y, Narsaiah K. Rapid point-of-care testing methods/devices for meat species identification: A review. Compr Rev Food Sci Food Saf 2020; 20:900-923. [PMID: 33443804 DOI: 10.1111/1541-4337.12674] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/30/2020] [Accepted: 10/25/2020] [Indexed: 12/15/2022]
Abstract
The authentication of animal species is an important issue due to an increasing trend of adulteration and mislabeling of animal species in processed meat products. Polymerase chain reaction is the most sensitive and specific technique for nucleic acid-based animal species detection. However, it is a time-consuming technique that requires costly thermocyclers and sophisticated labs. In recent times, there is a need of on-site detection by point-of-care (POC) testing methods and devices under low-resource settings. These POC devices must be affordable, sensitive, specific, user-friendly, rapid and robust, equipment free, and delivered to the end users. POC devices should also confirm the concept of micro total analysis system. This review discusses POC testing methods and devices that have been developed for meat species identification. Recent developments in lateral flow assay-based devices for the identification of animal species in meat products are also reviewed. Advancements in increasing the efficiency of lateral flow detection are also discussed.
Collapse
Affiliation(s)
- Yogesh Kumar
- Department of Agricultural Structures and Environmental Control, ICAR-Central Institute of Post-Harvest Engineering and Technology (CIPHET), Ludhiana, India
| | - Kairam Narsaiah
- Department of Agricultural Structures and Environmental Control, ICAR-Central Institute of Post-Harvest Engineering and Technology (CIPHET), Ludhiana, India
| |
Collapse
|
28
|
Triplex Real-Time PCR Approach for the Detection of Crucial Fungal Berry Pathogens- Botrytis spp., Colletotrichum spp. and Verticillium spp. Int J Mol Sci 2020; 21:ijms21228469. [PMID: 33187143 PMCID: PMC7697166 DOI: 10.3390/ijms21228469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 12/30/2022] Open
Abstract
Phytopathogens cause undeniably serious damage in agriculture by harming fruit cultivations and lowering harvest yields, which as a consequence substantially reduces food production efficiency. Fungi of the Botrytis, Colletotrichum and Verticillium genera are a main concern in berry production. However, no rapid detection method for detecting all of these pathogens simultaneously has been developed to date. Therefore, in this study, a multiplex real-time PCR assay for this purpose was established. Universal fungal primers for the D2 region of the large subunit ribosomal DNA and three multiplexable fluorogenic probes specific for the chosen fungi were designed and deployed. The triplex approach for the molecular detection of these fungi, which was developed in this study, allows for the rapid and effective detection of crucial berry pathogens, which contributes to a more rapid implementation of protective measures in plantations and a significant reduction in losses caused by fungal diseases.
Collapse
|
29
|
Lu HW, Sakamuri R, Kumar P, Ferguson TM, Doebler RW, Herrington KD, Talbot RP, Weigel KM, Nguyen FK, Cangelosi GA, Narita M, Boyle DS, Niemz A. Integrated nucleic acid testing system to enable TB diagnosis in peripheral settings. LAB ON A CHIP 2020; 20:4071-4081. [PMID: 33021611 PMCID: PMC7787164 DOI: 10.1039/d0lc00445f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
To facilitate treatment and limit transmission of tuberculosis (TB), new methods are needed to enable rapid and affordable diagnosis of the disease in high-burden low-resource settings. We have developed a prototype integrated nucleic acid testing device to detect Mycobacterium tuberculosis (M.tb) in sputum. The device consists of a disposable cartridge and compact, inexpensive instrument that automates pathogen lysis, nucleic acid extraction, isothermal DNA amplification and lateral flow detection. A liquefied and disinfected sputum sample is manually injected into the cartridge, and all other steps are automated, with a result provided in <1.5 h. Cell disruption and DNA extraction is executed within a four-port active valve containing a miniature bead blender (based on PureLyse® technology, Claremont BioSolutions LLC). The DNA-containing eluate is combined with dry master-mix reagents and target DNA is isothermally amplified. Amplified master-mix is then pumped into a lateral flow strip chamber for detection. The entire process is performed in a single-use closed-system cartridge to prevent amplicon carryover. For testing of M.tb-spiked sputum the system provided a limit of detection of 5 × 103 colony forming units (CFU) per mL. None of the negative sputum-only controls yielded a false-positive result. Testing of 45 clinical sputum specimens from TB cases and controls relative to a validated manual qPCR-based comparator method revealed a preliminary sensitivity of 90% and specificity of 96%. With further development, the herein described integrated nucleic acid testing device can enable TB diagnosis and treatment initiation in the same clinical encounter in near-patient low-resource settings of high TB burden countries.
Collapse
Affiliation(s)
- Hsiang-Wei Lu
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Rama Sakamuri
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Pranav Kumar
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| | - Tanya M Ferguson
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Robert W Doebler
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Keith D Herrington
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Ryan P Talbot
- Claremont BioSolutions, 1182 Monte Vista Ave # 11, Upland, CA 91786, USA
| | - Kris M Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Felicia K Nguyen
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Gerard A Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Masahiro Narita
- Seattle & King County Tuberculosis Control Clinic, Harborview Medical Center, 325 9th Ave, Seattle, WA 98104, USA
| | | | - Angelika Niemz
- Riggs School of Applied Life Sciences, Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| |
Collapse
|
30
|
Zhang YQ, Li XX, Li WB, Jiang JG, Zhang GL, Zhuang Y, Xu JY, Shi J, Sun DY. Analysis and predication of tuberculosis registration rates in Henan Province, China: an exponential smoothing model study. Infect Dis Poverty 2020; 9:123. [PMID: 32867846 PMCID: PMC7457775 DOI: 10.1186/s40249-020-00742-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/16/2020] [Indexed: 11/17/2022] Open
Abstract
Background The World Health Organization End TB Strategy meant that compared with 2015 baseline, the reduction in pulmonary tuberculosis (PTB) incidence should be 20 and 50% in 2020 and 2025, respectively. The case number of PTB in China accounted for 9% of the global total in 2018, which ranked the second high in the world. From 2007 to 2019, 854 672 active PTB cases were registered and treated in Henan Province, China. This study was to assess whether the WHO milestones could be achieved in Henan Province. Methods The active PTB numbers in Henan Province from 2007 to 2019, registered in Chinese Tuberculosis Information Management System were analyzed to predict the active PTB registration rates in 2020 and 2025, which is conductive to early response measures to ensure the achievement of the WHO milestones. The time series model was created by monthly active PTB registration rates from 2007 to 2016, and the optimal model was verified by data from 2017 to 2019. The Ljung-Box Q statistic was used to evaluate the model. The statistically significant level is α = 0.05. Monthly active PTB registration rates and 95% confidence interval (CI) from 2020 to 2025 were predicted. Results High active PTB registration rates in March, April, May and June showed the seasonal variations. The exponential smoothing winter’s multiplication model was selected as the best-fitting model. The predicted values were approximately consistent with the observed ones from 2017 to 2019. The annual active PTB registration rates were predicted as 49.1 (95% CI: 36.2–62.0) per 100 000 population and 34.4 (95% CI: 18.6–50.2) per 100 000 population in 2020 and 2025, respectively. Compared with the active PTB registration rate in 2015, the reduction will reach 23.7% (95% CI, 3.2–44.1%) and 46.8% (95% CI, 21.4–72.1%) in 2020 and 2025, respectively. Conclusions The high active PTB registration rates in spring and early summer indicate that high risk of tuberculosis infection in late autumn and winter in Henan Province. Without regard to the CI, the first milestone of WHO End TB Strategy in 2020 will be achieved. However, the second milestone in 2025 will not be easily achieved unless there are early response measures in Henan Province, China.
Collapse
Affiliation(s)
- Yan-Qiu Zhang
- Henan Center for Disease Control and Prevention, Zhengzhou, 450016, P. R. China.
| | - Xin-Xu Li
- Center for Drug Evaluation, National Medical Products Administration, Beijing, 100022, P. R. China
| | - Wei-Bin Li
- Kaifeng Municipal Health Commission, Kaifeng, 475000, P. R. China
| | - Jian-Guo Jiang
- Henan Center for Disease Control and Prevention, Zhengzhou, 450016, P. R. China
| | - Guo-Long Zhang
- Henan Center for Disease Control and Prevention, Zhengzhou, 450016, P. R. China
| | - Yan Zhuang
- Henan Center for Disease Control and Prevention, Zhengzhou, 450016, P. R. China
| | - Ji-Ying Xu
- Henan Center for Disease Control and Prevention, Zhengzhou, 450016, P. R. China
| | - Jie Shi
- Henan Center for Disease Control and Prevention, Zhengzhou, 450016, P. R. China
| | - Ding-Yong Sun
- Henan Center for Disease Control and Prevention, Zhengzhou, 450016, P. R. China
| |
Collapse
|
31
|
Silva Zatti M, Domingos Arantes T, Cordeiro Theodoro R. Isothermal nucleic acid amplification techniques for detection and identification of pathogenic fungi: A review. Mycoses 2020; 63:1006-1020. [PMID: 32648947 DOI: 10.1111/myc.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fungal infections have increased during the last years due to the AIDS epidemic and immunosuppressive therapies. The available diagnostic methods, such as culture, histopathology and serology, have several drawbacks regarding sensitivity, specificity and time-consuming, while molecular methods are still expensive and dependent on many devices. In order to overcome these challenges, isothermal nucleic acid amplification techniques (INAT) arose as promising diagnostic methods for infectious diseases. OBJECTIVE This review aimed to present and discuss the main contributions of the isothermal nucleic acid amplification techniques applied in medical mycology. METHODS Papers containing terms for each INAT (NASBA, RCA, LAMP, CPA, SDA, HAD or PSR) and the terms 'mycoses' or 'disease, fungal' were obtained from National Center for Biotechnology Information database until August 2019. RESULTS NASBA, RCA, LAMP and PSR are the INAT reported in the literature for detection and identification of pathogenic fungi. Despite the need of a previous conventional PCR, the RCA technique might also be used for genotyping or cryptic species differentiation, which may be important for the treatment of certain mycoses; nevertheless, LAMP is the most used INAT for pathogen detection. CONCLUSION Among all INATs herein reviewed, LAMP seems to be the most appropriate method for fungal detection, since it is affordable, sensitive, specific, user-friendly, rapid, robust, equipment-free and deliverable to end-users, fulfilling all ASSURED criteria of the World Health Organization for an ideal diagnostic method.
Collapse
Affiliation(s)
- Matheus Silva Zatti
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Thales Domingos Arantes
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiás, Brazil
| | - Raquel Cordeiro Theodoro
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
| |
Collapse
|
32
|
Gopalaswamy R, Shanmugam S, Mondal R, Subbian S. Of tuberculosis and non-tuberculous mycobacterial infections - a comparative analysis of epidemiology, diagnosis and treatment. J Biomed Sci 2020; 27:74. [PMID: 32552732 PMCID: PMC7297667 DOI: 10.1186/s12929-020-00667-6] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/05/2020] [Indexed: 12/26/2022] Open
Abstract
Pulmonary diseases due to mycobacteria cause significant morbidity and mortality to human health. In addition to tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), recent epidemiological studies have shown the emergence of non-tuberculous mycobacteria (NTM) species in causing lung diseases in humans. Although more than 170 NTM species are present in various environmental niches, only a handful, primarily Mycobacterium avium complex and M. abscessus, have been implicated in pulmonary disease. While TB is transmitted through inhalation of aerosol droplets containing Mtb, generated by patients with symptomatic disease, NTM disease is mostly disseminated through aerosols originated from the environment. However, following inhalation, both Mtb and NTM are phagocytosed by alveolar macrophages in the lungs. Subsequently, various immune cells are recruited from the circulation to the site of infection, which leads to granuloma formation. Although the pathophysiology of TB and NTM diseases share several fundamental cellular and molecular events, the host-susceptibility to Mtb and NTM infections are different. Striking differences also exist in the disease presentation between TB and NTM cases. While NTM disease is primarily associated with bronchiectasis, this condition is rarely a predisposing factor for TB. Similarly, in Human Immunodeficiency Virus (HIV)-infected individuals, NTM disease presents as disseminated, extrapulmonary form rather than as a miliary, pulmonary disease, which is seen in Mtb infection. The diagnostic modalities for TB, including molecular diagnosis and drug-susceptibility testing (DST), are more advanced and possess a higher rate of sensitivity and specificity, compared to the tools available for NTM infections. In general, drug-sensitive TB is effectively treated with a standard multi-drug regimen containing well-defined first- and second-line antibiotics. However, the treatment of drug-resistant TB requires the additional, newer class of antibiotics in combination with or without the first and second-line drugs. In contrast, the NTM species display significant heterogeneity in their susceptibility to standard anti-TB drugs. Thus, the treatment for NTM diseases usually involves the use of macrolides and injectable aminoglycosides. Although well-established international guidelines are available, treatment of NTM disease is mostly empirical and not entirely successful. In general, the treatment duration is much longer for NTM diseases, compared to TB, and resection surgery of affected organ(s) is part of treatment for patients with NTM diseases that do not respond to the antibiotics treatment. Here, we discuss the epidemiology, diagnosis, and treatment modalities available for TB and NTM diseases of humans.
Collapse
Affiliation(s)
- Radha Gopalaswamy
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | - Sivakumar Shanmugam
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | - Rajesh Mondal
- Department of Bacteriology, National Institute for Research in Tuberculosis, Chennai, India
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States.
| |
Collapse
|
33
|
Cross-priming isothermal amplification combined with nucleic acid test strips for detection of meat species. Anal Biochem 2020; 597:113672. [DOI: 10.1016/j.ab.2020.113672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 12/17/2022]
|
34
|
Zhai J, Yan Z, Ping F, Lei Q, Chen X, Qi Y. Establishment and application of isothermal amplification techniques for the detection of heat-stable I enterotoxin of enterotoxigenic Escherichia coli. PLoS One 2020; 15:e0230881. [PMID: 32315305 PMCID: PMC7173923 DOI: 10.1371/journal.pone.0230881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/10/2020] [Indexed: 01/19/2023] Open
Abstract
The aim of this study was to establish isothermal multiple self-matching initiated amplification (IMSA) and cross-priming amplification (CPA) methods to detect heat-stable I enterotoxin (STa)-producing enterotoxigenic Escherichia coli (ETEC). To avoid cross-contamination of aerosols, a closed independent isothermal amplification tube (IAT) was used to perform the assays. Optimal amplification conditions for IMSA and CPA were selected for specificity and sensitivity, respectively, and for clinical relevance. Both IMSA and CPA assays could specifically recognize all 3-STa positive strains in which they fluoresced green under UV light, but not in the 11 non-STa strains. The results of the sensitivity analysis indicated that the detection limit of the IMSA assay was 1.5 ×102 CFU, comparable to real-time PCR, but 10-fold more sensitive than CPA and LAMP. Further evaluation of the detection methods of swine diarrhea samples demonstrated that both could successfully identify the DNA of STa-producing ETEC in clinical specimens, consistent with LAMP and qPCR methods. The results demonstrated that the IMSA and CPA methods had high specificity and sensitivity with rapid detection of ETEC, so having great potential in clinical applications.
Collapse
Affiliation(s)
- Junjun Zhai
- Shaanxi Province Engineering & Technology Research Center of Shanbei Cashmere Goats, Yulin University, Yulin, Shanxi, China
| | - Zhang Yan
- College of Life Science, Yulin University, Yulin, Shanxi, China
| | - Feng Ping
- College of Life Science, Yulin University, Yulin, Shanxi, China
| | - Qu Lei
- Shaanxi Province Engineering & Technology Research Center of Shanbei Cashmere Goats, Yulin University, Yulin, Shanxi, China
| | - Xuelong Chen
- College of Animal Science, Anhui Science and Technology University, Fengyang, Anhui, China
- * E-mail: (XC); (YQ)
| | - Yanping Qi
- College of Animal Science, Anhui Science and Technology University, Fengyang, Anhui, China
- * E-mail: (XC); (YQ)
| |
Collapse
|
35
|
Ou A, Wang K, Mao Y, Yuan L, Ye Y, Chen L, Zou Y, Huang T. First Report on the Rapid Detection and Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) in Viable but Non-culturable (VBNC) Under Food Storage Conditions. Front Microbiol 2020; 11:615875. [PMID: 33488559 PMCID: PMC7817642 DOI: 10.3389/fmicb.2020.615875] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 11/23/2020] [Indexed: 02/05/2023] Open
Abstract
Formation of viable but non-culturable (VBNC) status in methicillin-resistant Staphylococcus aureus (MRSA) has never been reported, and it poses a significant concern for food safety. Thus, this study aimed to firstly develop a rapid, cost-effective, and efficient testing method to detect and differentiate MRSA strains in the VBNC state and further apply this in real food samples. Two targets were selected for detection of MRSA and toxin, and rapid isothermal amplification detection assays were developed based on cross-priming amplification methodology. VBNC formation was performed for MRSA strain in both pure culture and in artificially contaminated samples, then propidium monoazide (PMA) treatment was further conducted. Development, optimization, and evaluation of PMA-crossing priming amplification (CPA) were further performed on detection of MRSA in the VBNC state. Finally, application of PMA-CPA was further applied for detection on MRSA in the VBNC state in contaminated food samples. As concluded in this study, formation of the VBNC state in MRSA strains has been verified, then two PMA-CPA assays have been developed and applied to detect MRSA in the VBNC state from pure culture and food samples.
Collapse
Affiliation(s)
- Aifen Ou
- Department of Food, Guangzhou City Polytechnic, Guangzhou, China
| | - Kan Wang
- Center for Translational Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yanxiong Mao
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Yuan
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Yanrui Ye
- School of Biological Science and Engineering, South China University of Technology, Guangzhou, China
| | - Ling Chen
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, China
| | - Yimin Zou
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Yimin Zou,
| | - Tengyi Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
- Tengyi Huang,
| |
Collapse
|
36
|
Li X, Su Y, Chu H, Lyu S, Tian J, Xu W. Rapid strand replacement primer thermostat visual sensor based on Bst DNA polymerase and pyrophosphatase for detecting Vibrio parahaemolyticus. Food Chem 2019; 310:125955. [PMID: 31841941 DOI: 10.1016/j.foodchem.2019.125955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/22/2019] [Accepted: 11/24/2019] [Indexed: 11/17/2022]
Abstract
Vibrio parahaemolyticus is a major hidden danger of food safety. To develop a rapid, sensitive and on-site detecting method of Vibrio parahaemolyticus (V. parahaemolyticus), a strand replacement primer thermostat phosphate (SRPP) visual sensor was proposed, based on Bst DNA polymerase and pyrophosphatase. The novel strand replacement primer (SRP) facilitates chain substitution and to open a self-folding hairpin by adding region at its 3' end. Under the action of the SRP, a pair of external primers and two inner primers, target DNA is specifically amplified at 63 °C relies mainly on the hairpin. Many pyrophosphates (PPi) are simultaneously generated as by-products, which can be converted into phosphates (Pi) by pyrophosphatase for phosphomolybdate blue visual detection within 5 min. The proposed biosensor can detect 1.29 × 103 copies of V. parahaemolyticus within 35 min.
Collapse
Affiliation(s)
- Xuetong Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; College of Biological Science and Technology, Agricultural University of Shenyang, Shenyang 110866, China.
| | - Yuan Su
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Huashuo Chu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Shuxia Lyu
- College of Biological Science and Technology, Agricultural University of Shenyang, Shenyang 110866, China
| | - Jingjing Tian
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, China.
| |
Collapse
|
37
|
Zhang J, DI B, Shan H, Liu J, Zhou Y, Chen H, Hu L, Wu X, Bai Z. Rapid Detection of Bacillus cereus Using Cross-Priming Amplification. J Food Prot 2019; 82:1744-1750. [PMID: 31536421 DOI: 10.4315/0362-028x.jfp-19-156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Bacillus cereus is a spore-forming gastrointestinal pathogen that can cause life-threatening diseases. Here, a simple and effective assay to detect B. cereus was developed, using cross-priming amplification (CPA). Amplicons were detected using disposable cartridges that contained nucleic acid detection strips. The sensitivity of CPA assay for B. cereus was assessed using serial dilutions of genomic DNA, which indicated a detection limit of 3.6 × 101 CFU/mL. No cross-reactions were detected when genomic DNA extracted from 12 different B. cereus strains and 20 other bacterial foodborne strains were tested, suggesting that the assay is highly specific. Finally, we evaluated the practical applications of the CPA assay for the detection of B. cereus in 150 food samples and found that its sensitivity and specificity, compared with real-time PCR, were approximately 98.18 and 100%, respectively. In conclusion, CPA combined with nucleic acid detection strips is easy to perform, requires simple equipment, and offers highly specific and sensitive B. cereus detection.
Collapse
Affiliation(s)
- Jing Zhang
- Guangzhou Center for Disease Control and Prevention, 1 Qide Road, Guangzhou, 510440, Guangdong, People's Republic of China (ORCID: https://orcid.org/0000-0002-8377-2393 [Z.B.])
| | - Biao DI
- Guangzhou Center for Disease Control and Prevention, 1 Qide Road, Guangzhou, 510440, Guangdong, People's Republic of China (ORCID: https://orcid.org/0000-0002-8377-2393 [Z.B.])
| | - Hongbo Shan
- ADICON Clinical Laboratory, Inc., No. 398 Tianmushan Road, Hangzhou, 310023, Zhejiang, People's Republic of China
| | - Junhua Liu
- Guangzhou Center for Disease Control and Prevention, 1 Qide Road, Guangzhou, 510440, Guangdong, People's Republic of China (ORCID: https://orcid.org/0000-0002-8377-2393 [Z.B.])
| | - Yong Zhou
- Guangzhou Center for Disease Control and Prevention, 1 Qide Road, Guangzhou, 510440, Guangdong, People's Republic of China (ORCID: https://orcid.org/0000-0002-8377-2393 [Z.B.])
| | - Huiling Chen
- Guangzhou Center for Disease Control and Prevention, 1 Qide Road, Guangzhou, 510440, Guangdong, People's Republic of China (ORCID: https://orcid.org/0000-0002-8377-2393 [Z.B.])
| | - Lin Hu
- Ustar Biotechnologies (Hangzhou) Co., Ltd., 3766 Nanhuan Road, Hangzhou, 310012, Zhejiang, People's Republic of China
| | - Xinwei Wu
- Guangzhou Center for Disease Control and Prevention, 1 Qide Road, Guangzhou, 510440, Guangdong, People's Republic of China (ORCID: https://orcid.org/0000-0002-8377-2393 [Z.B.])
| | - Zhijun Bai
- Guangzhou Center for Disease Control and Prevention, 1 Qide Road, Guangzhou, 510440, Guangdong, People's Republic of China (ORCID: https://orcid.org/0000-0002-8377-2393 [Z.B.])
| |
Collapse
|
38
|
Rapid detection of giant salamander iridovirus by cross-priming amplification. J Virol Methods 2019; 274:113678. [PMID: 31442460 DOI: 10.1016/j.jviromet.2019.113678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/27/2019] [Accepted: 06/10/2019] [Indexed: 11/21/2022]
Abstract
Giant salamander iridovirus (GSIV) belongs to the epizootic genus Ranavirus, and is the cause of epidemic diseases associated with high mortality and great losses to artificial breeding and farming. Here, we established a simple, accurate, and reliable cross-priming amplification (CPA) method to detect GSIV. The CPA assay targets the major caspid protein gene of the GSIV genome to design crossing primer pairs, and the reaction conditions were optimized, including optimal concentrations of the primers, betaine, dNTPs, Mg2+, and Bst DNA polymerase, and reaction conditions. The sensitivity was shown to be 10 times higher than that of conventional polymerase chain reaction (PCR), and the specificity was 100%. The results were identified on nucleic acid strips within 3-5 min. Application of the CPA and PCR to 54 samples of giant salamander showed a positive rate of 72.22% and 74.07%, respectively, demonstrating high coincidence (94.44%, kappa = 8.7, P < 0.0001). The sensitivity of the CPA assay was 97.50% and the specificity was 92.86%. Thus, the CPA assay is as effective as conventional PCR, but with added practical advantages of simplicity and an almost instrument-free platform, which will be useful for both laboratories and giant salamander farms.
Collapse
|
39
|
Liu W, Yuan C, Zhang L, Feng Y. Establishment and application of isothermal multiple-self-matching-initiated amplification (IMSA) in detecting Type II heat-labile enterotoxin of Escherichia coli. PLoS One 2019; 14:e0216272. [PMID: 31048928 PMCID: PMC6497269 DOI: 10.1371/journal.pone.0216272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 04/17/2019] [Indexed: 01/02/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) constitutes a major cause of diarrhea in young children and animals, particularly in poor regions of the world, as well the traveler's diarrhea in adult individuals. Type II heat-labile enterotoxin (LT-II) from ETEC can cause profuse watery diarrhea, posing a potential threat to public health and animal husbandry. In the present study, isothermal multiple-self-matching-initiated amplification (IMSA) was established to rapidly detect LT-II producing ETEC. The specificity and sensitivity were assessed, and clinical samples were tested. The established IMSA method had good specificity for the detection of LT-II gene with a limit of detection of 25 CFU/mL, i.e. 2 times higher than that of real-time PCR and other two isothermal amplifications (loop-mediated isothermal amplification, LAMP and cross-primer isothermal amplification, CPA). Meanwhile, in 103 clinical Escherichia coli strains isolated from diarrhea samples, 9 strains with LT-II+ gene were detected (8.73%), corroborating real-time PCR, LAMP and CPA data. Therefore, the IMSA technology applied for the detection of LT-II producing ETEC has a good application prospect for screening clinical samples in primary medical units or common laboratories.
Collapse
Affiliation(s)
- Wenxin Liu
- Affiliated Central People’s Hospital of Zhanjiang, Zhanjiang, Guangdong, China
| | - Chaowen Yuan
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China
| | - Liguo Zhang
- Center for Animal Disease Emergency of Liaoning province, Shenyang, Liaoning, China
| | - Yufei Feng
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
- * E-mail:
| |
Collapse
|
40
|
Liu W, Yuan C, Zhang L, Feng Y. Development of isothermal amplification methods for rapid and sensitive detection of heat-labile enterotoxin producing Escherichia coli. J Microbiol Methods 2019; 161:47-55. [PMID: 31002853 DOI: 10.1016/j.mimet.2019.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/14/2019] [Accepted: 04/14/2019] [Indexed: 11/26/2022]
Abstract
The objective of this study was to establish a novel isothermal amplification method for detection of heat-labile enterotoxin (LT-I)-producing Escherichia coli. Loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and isothermal multiple-self-matching-initiated amplification (IMSA) were developed and evaluated. Optimal conditions, specificity, and sensitivity tests were performed and compared to qPCR findings. All three methods could produce ladder-like products with LT-I positive samples, while no products were generated with the negative controls. The amplified products could be directly visualized as negative or positive in the isothermal amplification (IAM) tube, which saved time and prevented the possibility of cross-contamination. The detection limits of each assay were similar, and all three assays could directly detect the DNA of Escherichia coli in clinical samples successfully. This is the first report on the application of CPA and IMSA methods for the detection of LT-I. The findings suggest that the three assays may be important tools for the rapid detection of enterotoxigenic Escherichia coli (ETEC) in the clinic.
Collapse
Affiliation(s)
- Wenxin Liu
- Affiliated Central People's Hospital of Zhanjiang, Zhanjiang 524045, PR China
| | - Chaowen Yuan
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, PR China
| | - Liguo Zhang
- Center for Animal Disease Emergency of Liaoning province, Shenyang 110161, PR China
| | - Yufei Feng
- Affiliated Hospital of Guangdong Medical University, Zhanjiang 524001, PR China.
| |
Collapse
|
41
|
Loop-mediated isothermal amplification (LAMP) approach for detection of heat-resistant Talaromyces flavus species. Sci Rep 2019; 9:5846. [PMID: 30971732 PMCID: PMC6458134 DOI: 10.1038/s41598-019-42275-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/27/2019] [Indexed: 11/29/2022] Open
Abstract
Talaromyces flavus is a soilborne fungus that can contaminate fruits. It constitutes serious influence on heat-processed food spoilage, as T. flavus belongs to the heat-resistant fungi group, which are able to survive the pasteurization process. Moreover T. flavus has been reported to be capable of mycotoxigenicity, therefore they have a serious threat to human health. To maintain the safety of food production, sensitive method for T. flavus detection was developed. The loop mediated amplification, abbreviated LAMP, reactions were designed as specific for detection of DNA replication licensing factor gene of T. flavus. The specificity of assay was confirmed by use of 5 T. flavus strains and 35 other fungal isolates. The achieved limit of detection was 1fg of T. flavus genomic DNA and 64 ascospores in 1 g of strawberry fruits or soil samples.
Collapse
|
42
|
Wang T, Liu Y, Sun HH, Yin BC, Ye BC. An RNA-Guided Cas9 Nickase-Based Method for Universal Isothermal DNA Amplification. Angew Chem Int Ed Engl 2019; 58:5382-5386. [PMID: 30773764 DOI: 10.1002/anie.201901292] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 12/11/2022]
Abstract
We have developed an ingenious method, termed Cas9 nickase-based amplification reaction (Cas9nAR), to amplify a target fragment from genomic DNA at a constant temperature of 37 °C. Cas9nAR employs a sgRNA:Cas9n complex with a single-strand nicking property, a strand-displacing DNA polymerase, and two primers bearing the cleavage sequence of Cas9n, to promote cycles of DNA replication through priming, extension, nicking, and displacement reaction steps. Cas9nAR exhibits a zeptomolar limit of detection (2 copies in 20 μL of reaction system) within 60 min and a single-base discrimination capability. More importantly, the underlying principle of Cas9nAR offers simplicity in primer design and universality in application. Considering the superior sensitivity and specificity, as well as the simple-to-implement, rapid, and isothermal features, Cas9nAR holds great potential to become a routine assay for the quantitative detection of nucleic acids in basic and applied studies.
Collapse
Affiliation(s)
- Ting Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Yong Liu
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Huan-Huan Sun
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang, 832000, China
| |
Collapse
|
43
|
Accuracy of Commercial Molecular Diagnostics for the Detection of Pulmonary Tuberculosis in China: A Systematic Review. Sci Rep 2019; 9:4553. [PMID: 30872692 PMCID: PMC6418248 DOI: 10.1038/s41598-019-41074-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/28/2019] [Indexed: 12/14/2022] Open
Abstract
This systematic review assesses the accuracy of molecular diagnostic methods for the detection of pulmonary tuberculosis in studies performed in China, published in Chinese and English. We searched for studies that assessed the accuracy of molecular diagnostics for pulmonary TB in China in the China National Knowledge Infrastructure, the Wanfang Database, SinoMed, VIP Information, Pubmed, Embase, and the Cochrane Library. For each index test, a summary estimation for sensitivity and specificity was calculated using the bivariate random-effects model. A total of 59 studies were included in our analysis. Loop-mediated isothermal amplifcation (LAMP) assay (six studies; pooled sensitivity 90%, 95% CI 78-95%; specificity 93%, 85-97%), line probe assay (LPA) (one study; 87%, 84-90%; 94%, 92-95%) and polymerase chain reaction (PCR) (FQ-PCR and RT-PCR) (four studies; 90%, 55-99%; 93%, 71-99%) showed good diagnostic performance in the meta-analysis. The highest pooled sensitivity was from Xpert MTB/RIF (20 studies; pooled sensitivity 91%, 95% CI 87-94%). The highest pooled specificity was from cross-priming amplification (CPA) (six studies; pooled specificity 97%, 95-99%). The lowest pooled sensitivity and specificity were from simultaneous amplification and testing (SAT)-TB (three studies; 79%, 66-88%; 72%, 48-88%). In subgroup analysis, molecular diagnostics demonstrated higher sensitivity for pulmonary TB detection in smear-positive specimens. Xpert MTB/RIF, LAMP, LPA, CPA and PCR demonstrated high accuracy overall for pulmonary tuberculosis detection, while SAT-TB had poor performance.
Collapse
|
44
|
Wang T, Liu Y, Sun H, Yin B, Ye B. An RNA‐Guided Cas9 Nickase‐Based Method for Universal Isothermal DNA Amplification. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ting Wang
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Yong Liu
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Huan‐Huan Sun
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Bin‐Cheng Yin
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Bang‐Ce Ye
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
- Institute of Engineering Biology and HealthCollaborative Innovation Center of Yangtze River Delta Region Green PharmaceuticalsCollege of Pharmaceutical SciencesZhejiang University of Technology Hangzhou 310014 Zhejiang China
- School of Chemistry and Chemical EngineeringShihezi University Xinjiang 832000 China
| |
Collapse
|
45
|
Ding X, Mauk MG, Yin K, Kadimisetty K, Liu C. Interfacing Pathogen Detection with Smartphones for Point-of-Care Applications. Anal Chem 2019; 91:655-672. [PMID: 30428666 PMCID: PMC6867037 DOI: 10.1021/acs.analchem.8b04973] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - Karteek Kadimisetty
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| |
Collapse
|
46
|
Mitsakakis K, D'Acremont V, Hin S, von Stetten F, Zengerle R. Diagnostic tools for tackling febrile illness and enhancing patient management. MICROELECTRONIC ENGINEERING 2018; 201:26-59. [PMID: 32287568 PMCID: PMC7114275 DOI: 10.1016/j.mee.2018.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Most patients with acute infectious diseases develop fever, which is frequently a reason to visit health facilities in resource-limited settings. The symptomatic overlap between febrile diseases impedes their diagnosis on clinical grounds. Therefore, the World Health Organization promotes an integrated management of febrile illness. Along this line, we present an overview of endemic and epidemic etiologies of fever and state-of-the-art diagnostic tools used in the field. It becomes evident that there is an urgent need for the development of novel technologies to fulfill end-users' requirements. This need can be met with point-of-care and near-patient diagnostic platforms, as well as e-Health clinical algorithms, which co-assess test results with key clinical elements and biosensors, assisting clinicians in patient triage and management, thus enhancing disease surveillance and outbreak alerts. This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem.
Collapse
Affiliation(s)
- Konstantinos Mitsakakis
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Corresponding author.
| | - Valérie D'Acremont
- Swiss Tropical and Public Health Institute, University of Basel, Socinstrasse 57, 4002 Basel, Switzerland
- Department of Ambulatory Care and Community Medicine, University of Lausanne, Bugnon 44, 1011 Lausanne, Switzerland
| | - Sebastian Hin
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- Laboratory for MEMS Applications, IMTEK – Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- BIOSS – Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
| |
Collapse
|
47
|
Wang YX, Zhang AY, Yang YQ, Lei CW, Cheng GY, Zou WC, Zeng JX, Chen YP, Wang HN. Sensitive and rapid detection of Salmonella enterica serovar Indiana by cross-priming amplification. J Microbiol Methods 2018; 153:24-30. [PMID: 30099005 DOI: 10.1016/j.mimet.2018.08.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 11/28/2022]
Abstract
Salmonella enterica serovar Indiana (S. Indiana) was the most frequently reported foodborne pathogen, which has a broad host range including poultry, swine, and humans. Traditional methods used for the detection of S. Indiana from contaminated food products are time-consuming and labor-intensive. Therefore, rapid detection methods with high sensitivity and specificity are vitally important to prevent the spread of S. Indiana. In this study, we developed a nearly instrument-free, simple molecular method which incorporates cross-priming amplification (CPA) combined with a nucleic acid detection strip (NADS) for sensitive detection of S. Indiana. A set of CPA primers was designed based on S. Indiana specific nucleotide sequences and the specificity of CPA-NADS was tested against 42 bacterial strains. The results showed that this method was highly specific for detection of S. Indiana. The sensitivity of CPA-NADS was evaluated and compared with that of the serovar-specific PCR method and the real-time PCR method. The limit of detection of the CPA method was 8.997 fg/μL for genomic DNA and 6.2 × 101 CFU/mL for bacteria in pure culture. An application of the CPA assay was conducted with 90 inoculated specimens by S. Indiana. The accuracy of CPA-NADS was consistent with the results of the traditional culture-based methods in inoculated specimens. This method showed a higher sensitivity than the serovar-specific PCR method did and was more convenient to perform. In conclusion, we demonstrated that the CPA-NADS system offers high specificity, sensitivity, rapidity, and a simple detection tool for screening S. Indiana.
Collapse
Affiliation(s)
- Yong-Xiang Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China
| | - An-Yun Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China
| | - Yong-Qiang Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China
| | - Chang-Wei Lei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China
| | - Guang-Yang Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China
| | - Wen-Cheng Zou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China
| | - Jin-Xin Zeng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China
| | - Yan-Peng Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China
| | - Hong-Ning Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610065, Sichuan, PR China; "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Sichuan University, Chengdu 610065, Sichuan, PR China.
| |
Collapse
|
48
|
Eddabra R, Ait Benhassou H. Rapid molecular assays for detection of tuberculosis. Pneumonia (Nathan) 2018; 10:4. [PMID: 29876241 PMCID: PMC5968606 DOI: 10.1186/s41479-018-0049-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an important public health problem at the global level. It is one of the main causes of morbidity and mortality, due to the emergence of antibiotic resistant Mycobacterium strains and HIV co-infection. Over the past decade, important progress has been made for better control of the disease. While microscopy and culture continue to be indispensible for laboratory diagnosis of tuberculosis, the range of several molecular diagnostic tests, including the nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have expanded tremendously. They are becoming more accessible not only for detection and identification of Mycobacterium tuberculosis complex in clinical specimens, but now extend to diagnosing multi-drug resistant strains. Molecular diagnostic tests provide timely results useful for high-quality patient care, low contamination risk, and ease of performance and speed. This review focuses on the current diagnostic tests in use, including emerging technologies used for detection of tuberculosis in clinical specimens. The sensitivity and specificity of these tests have also been taken into consideration.
Collapse
Affiliation(s)
- Rkia Eddabra
- Higher Institute of Nursing Professions and Health Techniques, Avenue Colonnel Major Habbouha Oueld Laâbid. Madinat Al Wahda I, Laayoune, Morocco
| | - Hassan Ait Benhassou
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100 Rabat, Morocco
| |
Collapse
|
49
|
Mao R, Qi L, Wang Z, Liu H, Du Y. Helix loop-mediated isothermal amplification of nucleic acids. RSC Adv 2018; 8:19098-19102. [PMID: 35539645 PMCID: PMC9080610 DOI: 10.1039/c8ra01201f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/07/2018] [Indexed: 11/21/2022] Open
Abstract
Isothermal nucleic acid amplification has played a key role in the point of care test (POCT). In this study, a helix loop-mediated isothermal amplification (HAMP) method with high specificity, efficiency and rapidity was developed. The MERS-Cov orf1b gene was chosen for the validation and optimization of HAMP. The HAMP analysis was performed at a constant temperature of 61-65 °C and yielded a self-primed spiral structure with no introduction of exogenous gene sequence by two pairs of specially designed primers. The primers for helix loop formation were composed of two complementary primers including the helix forward primer and the helix reverse primer, the 3' ends of which were complementary to their respective target nucleic acids. HAMP assay can be monitored by fluorescence signals with the addition of Eva Green in the reaction mixture. In addition, an accelerated HAMP was developed after the addition of acceleration probe, which could be finished within 75 min with a sensitivity of 10 copies per reaction. Further, a reverse transcription-HAMP (RT-HAMP) was proven to be feasible for RNA detection by combining the reverse transcriptase with DNA polymerase. Finally, both the HAMP and RT-HAMP assay were visually conducted by using Hydroxynaphthol blue (HNB) as a chromogenic indicator. All in all, it is suggested that the HAMP assay would have great potential in POCT applications.
Collapse
Affiliation(s)
- Rui Mao
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 P. R. China +86-10-82545070 +86-10-82545070.,University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Lifei Qi
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 P. R. China +86-10-82545070 +86-10-82545070.,University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Zhuo Wang
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 P. R. China +86-10-82545070 +86-10-82545070
| | - Hongtao Liu
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 P. R. China +86-10-82545070 +86-10-82545070.,Zhengzhou Institute of Emerging Industrial Technology Zhengzhou 450000 P. R. China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 P. R. China +86-10-82545070 +86-10-82545070
| |
Collapse
|
50
|
Gupta S, Kakkar V. Recent technological advancements in tuberculosis diagnostics - A review. Biosens Bioelectron 2018; 115:14-29. [PMID: 29783081 DOI: 10.1016/j.bios.2018.05.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/26/2018] [Accepted: 05/09/2018] [Indexed: 01/14/2023]
Abstract
Early diagnosis and on-time effective treatment are indispensable for Tuberculosis (TB) control - a life threatening infectious communicable disease. The conventional techniques for diagnosing TB normally take two to three weeks. This delay in diagnosis and further increase in detection complexity due to the emerging risks of XDR-TB (Extensively drug Resistant-TB) and MDR-TB (Multidrug Resistant-TB) are evoking interest of researchers in the field of developing rapid TB detection techniques such as biosensing and other point-of-care (POC) techniques. Biosensing technologies along with the collaboration with nanotechnology have enormous potential to boost the MTB detection and for overall management in clinical diagnosis. A diverse range of portable, sensitive and rapid biosensors based on different signal transducer principles and with different biomarkers detection capabilities have been developed for TB detection in the early stages. Further, a lot of progress has been achieved over the years in developing various point-of-care diagnostic tools including non-molecular methods and molecular techniques. The objective of this study is to present a succinct review of the available TB detection techniques that are either in use or under development. The focus of this review is on the current developments occurred in nano-biosensing technologies. A synopsis of ameliorations in different non-molecular diagnostic tools and progress in the field of molecular techniques along with the role of emerging Lab-on-Chip technology for diagnosing and mitigating the TB consequences have also been presented.
Collapse
Affiliation(s)
- Shagun Gupta
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra 182320, India.
| | - Vipan Kakkar
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra 182320, India.
| |
Collapse
|