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Gu X, Tang Q, Zhu Y, Sun C, Wu L, Ji H, Wang Q, Wu L, Qin Y. Advancements of CRISPR technology in public health-related analysis. Biosens Bioelectron 2024; 261:116449. [PMID: 38850734 DOI: 10.1016/j.bios.2024.116449] [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: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Pathogens and contaminants in food and the environment present significant challenges to human health, necessitating highly sensitive and specific diagnostic methods. Traditional approaches often struggle to meet these requirements. However, the emergence of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has revolutionized nucleic acid diagnostics. The present review provides a comprehensive overview of the biological sensing technology based on the CRISPR/Cas system and its potential applications in public health-related analysis. Additionally, it explores the enzymatic cleavage capabilities mediated by Cas proteins, highlighting the promising prospects of CRISPR technology in addressing bioanalysis challenges. We discuss commonly used CRISPR-Cas proteins and elaborate on their application in detecting foodborne bacteria, viruses, toxins, other chemical pollution, and drug-resistant bacteria. Furthermore, we highlight the advantages of CRISPR-based sensors in the field of public health-related analysis and propose that integrating CRISPR-Cas biosensing technology with other technologies could facilitate the development of more diverse detection platforms, thereby indicating promising prospects in this field.
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Affiliation(s)
- Xijuan Gu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China; Xinglin College, Nantong University, Qidong, Jiangsu, 226236, PR China
| | - Qu Tang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Yidan Zhu
- Medical School, Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Chenling Sun
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Lingwei Wu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Haiwei Ji
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Qi Wang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, PR China; School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Yuling Qin
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
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2
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Dou S, Liu M, Wang H, Zhou S, Marrazza G, Guo Y, Sun X, Darwish IA. Synthesis of dual models multivalent activatable aptamers based on HCR and RCA for ultrasensitive detection of Salmonella typhimurium. Talanta 2024; 275:126101. [PMID: 38631268 DOI: 10.1016/j.talanta.2024.126101] [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: 02/19/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
Aptamers have superior structural properties and have been widely used in bacterial detection methods. However, the problem of low affinity still exists in complex sample detection. In contrast, hybridization chain reaction (HCR)-based model I and rolling circle amplification (RCA)-based model II multivalent activatable aptamers (multi-Apts) can fulfill the need for low-cost, rapid, highly sensitive and high affinity detection of S. typhimurium. In our research, two models of multi-Apts were designed. First, a monovalent activatable aptamer (mono-Apt) was constructed by fluorescence resonance energy transfer (FRET) with an S. typhimurium aptamer and its complementary chain of BHQ1. Next, the DNA scaffold was obtained by HCR and RCA, and the multi-Apts were obtained by self-assembly of the mono-Apt with a DNA scaffold. In model I, when target was presented, the complementary chain BHQ1 was released due to the binding of multi-Apts to the target and was subsequently adsorbed by UIO66. Finally, a FRET-based fluorescence detection signal was obtained. In mode II, the multi-Apts bound to the target, and the complementary chain BHQ1 was released to become the trigger chain for the next round of amplification of HCR with a fluorescence detection signal. HCR and RCA based multi-Apts were able to detect S. typhimurium as low as 2 CFU mL-1 and 1 CFU mL-1 respectively. Multi-Apts amplification strategy provides a new method for early diagnosis of pathogenic microorganisms in foods.
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Affiliation(s)
- Shouyi Dou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Mengyue Liu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Haifang Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Shuxian Zhou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Giovanna Marrazza
- "Ugo Schiff" Chemistry Department, University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy
| | - Yemin Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Xia Sun
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Ibrahim A Darwish
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
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3
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Yin L, Huo B, Xia L, Li G. On-Chip Capture, Raman-Silent Polymer Labeling, and Digital Mapping Analysis of Escherichia coli O157:H7 in Beverages All-in-One. Anal Chem 2024; 96:11036-11043. [PMID: 38934556 DOI: 10.1021/acs.analchem.4c01804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Escherichia coli O157:H7 is one of the most susceptible foodborne pathogens, easily causing food poisoning and other health risks. It is of great significance to establish a quantitative method with higher sensitivity and less time consumption for foodborne pathogens analysis. The Raman-silent signal has a good performance for avoiding interference from the food matrix so as to achieve accurate signal differentiation. In this work, we presented a preparation-mapping all-in-one method for digital mapping analysis. We prepared a functionalized Raman-silent polymer label of Escherichia coli O157:H7, which was captured on a porous 4-mercaptophenylboric acid@Ag foam chip. To improve accuracy and widen the detection range, a digital mapping quantitative strategy was employed in data extraction and processing. By transfer mapping information into digitized statistical results, the limitation of obtaining reproducible intensity values just by randomly selected spots on the substrate can be addressed. With a wide linear range of 1.0 × 101-1.0 × 105 CFU mL-1 and a limit of detection of 4.4 CFU mL-1, this all-in-one method had good sensitivity performance. Also, this method achieved good precision and selectivity in a series of experiments and was successfully applied to the analysis of beverage samples.
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Affiliation(s)
- Linhua Yin
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Bingyang Huo
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Ling Xia
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
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Dou S, Zhou S, Wang H, Liu M, Wang Y, Sun X, Guo Y. UIO66 low background signal and fluorescence synergism strategy for highly sensitive detection of Salmonella typhimurium. Talanta 2024; 274:126013. [PMID: 38569373 DOI: 10.1016/j.talanta.2024.126013] [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: 01/31/2024] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Successful construction of a detection method for Salmonella typhimurium (S. typhimurium) based on the synergy of hybridization chain reaction (HCR) and fluorescence was realized in this paper. First, the aptamer modified with the quenching group Black Hole Quencher-1 acid (BHQ1) was immobilized on the magnetic beads in combination with the complementary chain of the aptamer modified with 6-carboxyfluorescein (6-FAM). Second, S. typhimurium and cDNA-6-FAM immobilized on magnetic beads competitively bound to the aptamer. Finally, the cDNA-6-FAM was released after magnetic separation acted as a promoter to trigger HCR amplification when the target presented. The fluorescence signal could be significantly improved by the combination of green SYBR Green I (SGI) and HCR long double-stranded DNA and the fluorescent synergy of 6-FAM and SGI. Because of the separation of target and its aptamer, the trigger strand was abstracted by magnetic separation. There was no HCR to generate long double-stranded DNA, and the fluorescence of excess hairpin/SGI could be adsorbed through UIO66 so that only a very low background signal was detected. This fluorescent sensor was capable of monitoring S. typhimurium in the range of 10-3.2 × 107 CFU mL-1 with a limit of detection as low as 1.5 CFU mL-1. Because of the excellent properties of the aptasensor and the validity of SGI fluorescence synergy, this HCR enzyme-free amplification strategy could be generalized to other areas.
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Affiliation(s)
- Shouyi Dou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Shuxian Zhou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Haifang Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Mengyue Liu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Yinghui Wang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Xia Sun
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Yemin Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
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Gu X, Tang Q, Kang X, Ji H, Shi X, Shi L, Pan A, Zhu Y, Jiang W, Zhang J, Liu J, Wu M, Wu L, Qin Y. A portable CRISPR-Cas12a triggered photothermal biosensor for sensitive and visual detection of Staphylococcus aureus and Listeria monocytogenes. Talanta 2024; 271:125678. [PMID: 38277968 DOI: 10.1016/j.talanta.2024.125678] [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: 10/31/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
The detection of foodborne pathogens is crucial for ensuring the maintenance of food safety. In the present study, a portable CRISPR-Cas12a triggered photothermal biosensor integrating branch hybrid chain reaction (bHCR) and DNA metallization strategy for sensitive and visual detection of foodborne pathogens was proposed. The sheared probes were utilized to block the locker probes, which enabled preventing the assembly of bHCR in the absence of target bacteria, while target bacteria can activate the cleavage of sheared probes through CRISPR-Cas12a. Therefore, the locker probes functioned as initiating chains, triggering the formation of the branching double-stranded DNA consisting of H1, H2, and H3. The silver particles, which were in situ deposited on the DNA structure, functioned as a signal factor for conducting photothermal detection. Staphylococcus aureus and Listeria monocytogenes were selected as the foodborne pathogens to verify the analytical performance of this CRISPR-Cas12a triggered photothermal sensor platform. The sensor exhibited a sensitive detection with a low detection limit of 1 CFU/mL, while the concentration ranged from 100 to 108 CFU/mL. Furthermore, this method could efficiently detect target bacteria in multiple food samples. The findings demonstrate that this strategy can serve as a valuable reference for the development of a portable platform enabling quantitative analysis, visualization, and highly sensitive detection of foodborne bacteria.
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Affiliation(s)
- Xijuan Gu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China; Xinglin College, Nantong University, Qidong, Jiangsu, 226236, China
| | - Qu Tang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Xiaoxia Kang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Huoyan Ji
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Xiuying Shi
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Linyi Shi
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Anli Pan
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Yidan Zhu
- Medical School, Nantong University, Nantong, Jiangsu, 226001, China
| | - Wenjun Jiang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Jing Zhang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Jinxia Liu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China
| | - Mingmin Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China.
| | - Yuling Qin
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, China.
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6
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Lan H, Shu W, Jiang D, Yu L, Xu G. Cas-based bacterial detection: recent advances and perspectives. Analyst 2024; 149:1398-1415. [PMID: 38357966 DOI: 10.1039/d3an02120c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Persistent bacterial infections pose a formidable threat to global health, contributing to widespread challenges in areas such as food safety, medical hygiene, and animal husbandry. Addressing this peril demands the urgent implementation of swift and highly sensitive detection methodologies suitable for point-of-care testing and large-scale screening. These methodologies play a pivotal role in the identification of pathogenic bacteria, discerning drug-resistant strains, and managing and treating diseases. Fortunately, new technology, the CRISPR/Cas system, has emerged. The clustered regularly interspaced short joint repeats (CRISPR) system, which is part of bacterial adaptive immunity, has already played a huge role in the field of gene editing. It has been employed as a diagnostic tool for virus detection, featuring high sensitivity, specificity, and single-nucleotide resolution. When applied to bacterial detection, it also surpasses expectations. In this review, we summarise recent advances in the detection of bacteria such as Mycobacterium tuberculosis (MTB), methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli (E. coli), Salmonella and Acinetobacter baumannii (A. baumannii) using the CRISPR/Cas system. We emphasize the significance and benefits of this methodology, showcasing the capability of diverse effector proteins to swiftly and precisely recognize bacterial pathogens. Furthermore, the CRISPR/Cas system exhibits promise in the identification of antibiotic-resistant strains. Nevertheless, this technology is not without challenges that need to be resolved. For example, CRISPR/Cas systems must overcome natural off-target effects and require high-quality nucleic acid samples to improve sensitivity and specificity. In addition, limited applicability due to the protospacer adjacent motif (PAM) needs to be addressed to increase its versatility. Despite the challenges, we are optimistic about the future of bacterial detection using CRISPR/Cas. We have already highlighted its potential in medical microbiology. As research progresses, this technology will revolutionize the detection of bacterial infections.
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Affiliation(s)
- Huatao Lan
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Weitong Shu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Dan Jiang
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Luxin Yu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
| | - Guangxian Xu
- The First Dongguan Affiliated Hospital, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China.
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Zeng D, Jiao J, Mo T. Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection. Front Microbiol 2024; 15:1355234. [PMID: 38380103 PMCID: PMC10877009 DOI: 10.3389/fmicb.2024.1355234] [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: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.
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Affiliation(s)
| | | | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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Li Y, Jia J, Man S, Ye S, Ma L. Emerging programmable nuclease-based detection for food safety. Trends Biotechnol 2024; 42:151-155. [PMID: 37806898 DOI: 10.1016/j.tibtech.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
Food safety issues are an important challenge across the world. Programmable nucleases are emerging as new tools because of their significant biological advantages. This forum article provides an overview of recent advances and challenges in the novel paradigm of programmable nuclease-based detection for food safety.
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Affiliation(s)
- Yaru Li
- Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin, 300457, China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Jingyu Jia
- Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin, 300457, China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuli Man
- Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin, 300457, China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Shengying Ye
- Pharmacy Department, The 983th Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army, Tianjin, 300142, China.
| | - Long Ma
- Key Laboratory of Industrial Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China; State Key Laboratory of Food Nutrition and Safety, Tianjin, 300457, China; Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin, 300457, China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China.
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Liu S, Huo Y, Hu Z, Cao G, Gao Z. A label-free ratiometric fluorescent aptasensor based on a peroxidase-mimetic multifunctional ZrFe-MOF for the determination of tetrodotoxin. Mikrochim Acta 2023; 191:57. [PMID: 38153525 DOI: 10.1007/s00604-023-06118-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 12/29/2023]
Abstract
A Fe/Zr bimetal-organic framework (ZrFe-MOF) is utilized to establish a ratiometric fluorescent aptasensor for the determination of tetrodotoxin (TTX). The multifunctional ZrFe-MOF possesses inherent fluorescence at 445 nm wavelength, peroxidase-mimetic activity, and specific recognition and adsorption capabilities for aptamers, owing to its organic ligand, and Fe and Zr nodes. The peroxidation of o-phenylenediamine (OPD) substrate generates fluorescent 2,3-diaminophenazine (OPDox) at 555 nm wavelength, thus quenching the inherent fluorescence of ZrFe-MOF because of the fluorescence resonance energy transfer (FRET) effect. TTX aptamers, which are absorbed on the material surface without immobilization or fluorescent labeling, inhibit the peroxidase-mimetic activity of ZrFe-MOF. It causes the decreased OPDox fluorescence at 555 nm wavelength and the inverse restoration of ZrFe-MOF fluorescence at 445 nm wavelength. With TTX, the aptamers specifically bind to TTX, triggering rigid complex release from ZrFe-MOF surface and reactivating its peroxidase-mimetic activity. Consequently, the two fluorescence signals exhibit opposite changes. Employing this ratiometric strategy, the determination of TTX is achieved with a detection limit of 0.027 ng/mL and a linear range of 0.05-500 ng/mL. This aptasensor also successfully determines TTX concentrations in puffer fish and clam samples, demonstrating its promising application for monitoring trace TTX in food safety.
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Affiliation(s)
- Sha Liu
- Binzhou Medical University, Yantai, 264003, China
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yapeng Huo
- Yantai Center for Disease Control and Prevention, Yantai, 264003, China
| | - Zhiyong Hu
- Binzhou Medical University, Yantai, 264003, China
| | - Gaofang Cao
- Binzhou Medical University, Yantai, 264003, China.
| | - Zhixian Gao
- Binzhou Medical University, Yantai, 264003, China.
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
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Zhang Y, Gao L, Han J, Miao X. Dual-signal and one-step monitoring of Staphylococcus aureus in milk using hybridization chain reaction based fluorescent sensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123191. [PMID: 37517267 DOI: 10.1016/j.saa.2023.123191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/06/2023] [Accepted: 07/22/2023] [Indexed: 08/01/2023]
Abstract
Food-borne pathogens in dairy products that was contaminated from raw ingredients or improper food handling can cause a major threaten to human health. Here, to construct the pathogens detection, a dual-signal readout fluorescent switching sensor was designed for one-step determination of Staphylococcus aureus (S. aureus), which was a marker of food contamination. Graphene oxide (GO) was used as a fluorescence quencher, while fluorophore-labeled hairpin DNA was used as a donor, resulting in fluorescence resonance energy transfer (FRET) from the fluorophore to GO (signal off). Enzyme-free hybridization chain reaction could generate remarkable signal amplification, which avoided the nonspecific desorption caused by any enzymatic proteins in GO surface. With the strong binding ability of aptamer to S. aureus, a long bifluorescent molecules-labeled double-stranded DNA product was formed, bringing in dual-signal readout responses (signal on). Consequently, a reliable, sensitive and selective sensor was obtained for one-step quantification of S. aureus concentration from 10 to 108 CFU/mL with a detection limit of 1 CFU/mL. Furthermore, satisfactory stability, reproducibility, specificity and good recovery efficiency in milk samples revealed that the proposed sensor could be served as a prospective tool for food safety analysis.
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Affiliation(s)
- Yun Zhang
- Department of Pharmacy, Changzhi Medical College, Shanxi 046012, China.
| | - Liang Gao
- Department of Pharmacy, Changzhi Medical College, Shanxi 046012, China
| | - Jing Han
- Department of Pharmacy, Changzhi Medical College, Shanxi 046012, China
| | - Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, China
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11
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Guliy OI, Karavaeva OA, Smirnov AV, Eremin SA, Bunin VD. Optical Sensors for Bacterial Detection. SENSORS (BASEL, SWITZERLAND) 2023; 23:9391. [PMID: 38067765 PMCID: PMC10708710 DOI: 10.3390/s23239391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Analytical devices for bacterial detection are an integral part of modern laboratory medicine, as they permit the early diagnosis of diseases and their timely treatment. Therefore, special attention is directed to the development of and improvements in monitoring and diagnostic methods, including biosensor-based ones. A promising direction in the development of bacterial detection methods is optical sensor systems based on colorimetric and fluorescence techniques, the surface plasmon resonance, and the measurement of orientational effects. This review shows the detecting capabilities of these systems and the promise of electro-optical analysis for bacterial detection. It also discusses the advantages and disadvantages of optical sensor systems and the prospects for their further improvement.
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Affiliation(s)
- Olga I. Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms—Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), Saratov 410049, Russia;
| | - Olga A. Karavaeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms—Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), Saratov 410049, Russia;
| | - Andrey V. Smirnov
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Moscow 125009, Russia;
| | - Sergei A. Eremin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119991, Russia;
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12
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He Y, Hu Q, San S, Kasputis T, Splinter MGD, Yin K, Chen J. CRISPR-based Biosensors for Human Health: A Novel Strategy to Detect Emerging Infectious Diseases. Trends Analyt Chem 2023; 168:117342. [PMID: 37840598 PMCID: PMC10571337 DOI: 10.1016/j.trac.2023.117342] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Infectious diseases (such as sepsis, influenza, and malaria), caused by various pathogenic bacteria and viruses, are widespread across the world. Early and rapid detection of disease-related pathogens is necessary to reduce their spread in the world and prevent their potential global pandemics. The clustered regularly interspaced short palindromic repeats (CRISPR) technology, as the next-generation molecular diagnosis technique, holds immense promise in the detection of infectious diseases because of its remarkable advantages, including supreme flexibility, sensitivity, and specificity. While numerous CRISPR-based biosensors have been developed for application in environmental monitoring, food safety, and point-of-care diagnosis, there remains a critical need to summarize and explore their potential in human health. This review aims to address this gap by focusing on the latest advancements in CRISPR-based biosensors for infectious disease detection. We provide an overview of the current status, pre-amplification methods, the unique feature of each CRISPR system, and the design of CRISPR-based biosensing strategies to detect disease-associated nucleic acids. Last but not least, the review analyzes the current challenges and provides future perspectives, which will contribute to developing more effective CRISPR-based biosensors for human health.
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Affiliation(s)
- Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People’s Republic of China
| | - Samantha San
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Tom Kasputis
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People’s Republic of China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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13
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Yinur D, Moges B, Hassen A, Tessema TS. Loop mediated isothermal amplification as a molecular diagnostic assay: Application and evaluation for detection of Enterohaemorrhagic Escherichia coli (O157:H7). Pract Lab Med 2023; 37:e00333. [PMID: 37693632 PMCID: PMC10492192 DOI: 10.1016/j.plabm.2023.e00333] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose This study aimed at evaluating the performance of the Loop Mediated Isothermal Amplification (LAMP) diagnostic test, which targets the putative Fimbria protein-encoding gene (Z3276) for rapid and specific detection of locally isolated enterohemorrhagic Escherichia coli (EHEC) O157:H7. Results A total number of 40 locally available bacteria isolates and standard strains, among them 6 entrohemorrhagic (O157:H7) and 10 entropathogenic E. coli, 7 non diarrheic E. coli strains and 13 non entrohemorrhagic shiga toxic (stx) E. coli isolates as well as 4 pathogenic non E. coli species were used to optimize and evaluate the LAMP assay. The LAMP amplified DNA samples were visualized as turbid DNA both by naked eye and gel electrophoresis followed by staining. The assay had a sensitivity of 100% (6/6), a specificity of 97.05% (33/34), and an efficiency of 97.5% (39/40). The assay was also exhibited with 100% negative predicted value and 85.7% positive predicted value. The LAMP assay was also 10-fold more sensitive than the conventional PCR assay; sensitivity was determined by serial dilution. The results of LAMP and the PCR tests showed very high agreement (k = 0.97) in the detection of the bacteria studied. Conclusion Compared with the performance of PCR and SMAC, LAMP assay was better in terms of efficiency, rapidity and cost-effectiveness, which can be used as a point-care diagnostic test in resource-limited laboratories.
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Affiliation(s)
- Degisew Yinur
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Biniam Moges
- Department of Biotechnology, Debre Berhan University, Debre Berhan, Ethiopia
| | - Aliyi Hassen
- Department of Biotechnology, Ambo University, Ambo, Ethiopia
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14
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Dou S, Liu M, Zhang F, Li B, Zhang Y, Li F, Guo Y, Sun X. Silver/copper bimetallic nanoclusters integrating with cryonase-assisted target recycling amplification detection of Salmonella typhimurium. Mikrochim Acta 2023; 190:403. [PMID: 37728643 DOI: 10.1007/s00604-023-05973-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/27/2023] [Indexed: 09/21/2023]
Abstract
An unsophisticated fluorescence-enabled strategy is brought forward to process the highly sensitive fluorescence detection of Salmonella typhimurium (S. typhimurium) which based on polyethyleneimine (PEI)-templated silver/copper nanoclusters (Ag/CuNCs) (λ excitation = 334 nm and λ emission = 466 nm) with cryonase-assisted target recycling amplification. The Ag/CuNCs nanoclusters are synthesized as fluorescent materials due to their strong and stable fluorescence characteristics and are modified with S. typhimurium aptamers to form aptamer-Ag/CuNCs probes. The probes can be adsorbed on the surface of quenching agents-polydopamine nanospheres (PDANSs), thereby inducing fluorescence quenching of the probes. Once the aptamers are bound to the target, the aptamers/targets complexes are separated from the PDANSs surface, and the Ag/CuNCs recover the fluorescence signal. The released complexes will immediately be transformed into a substrate digested by cryonase (an enzyme that can digest all types of nucleic acids), and the released targets are bound to another aptamers to initiate the next round of cleavage. This reaction will be repeated continuously until all relevant aptamers are consumed and all Ag/CuNCs are released, resulting in a significant amplification of the fluorescence signal and improved sensitivity. Using Ag/CuNCs as fluorescent probes combined with cryonase-assisted amplification strategy, the fluorescence aptasensor is constructed with detection limits as low as 3.8 CFU mL-1, which is tenfold better than without the cryonase assistance. The method developed has been applied to milk, orange juice, chicken, and egg white samples with excellent selectivity and accuracy providing an approach for the early and rapid detection of S. typhimurium in food.
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Affiliation(s)
- Shouyi Dou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
| | - Mengyue Liu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
| | - Fengjuan Zhang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
| | - Baoxin Li
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
| | - Yuhao Zhang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
| | - Falan Li
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China
| | - Yemin Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China.
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China.
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China.
| | - Xia Sun
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China.
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China.
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, 255049, Shandong, China.
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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: 0] [Impact Index Per Article: 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.
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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
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16
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Zhang QB, Zhu P, Zhang S, Rong YJ, Huang ZA, Sun LW, Cai T. Hypervirulent Klebsiella pneumoniae detection methods: a minireview. Arch Microbiol 2023; 205:326. [PMID: 37672079 DOI: 10.1007/s00203-023-03665-y] [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: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/07/2023]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp), characterized by high virulence and epidemic potential, has become a global public health challenge. Therefore, improving the identification of hvKp and enabling earlier and faster detection in the community to support subsequent effective treatment and prevention of hvKp are an urgent issue. To address these issues, a number of assays have emerged, such as String test, Galleria mellonella infection test, PCR, isothermal exponential amplification, and so on. In this paper, we have collected articles on the detection methods of hvKp and conducted a retrospective review based on two aspects: traditional detection technology and biomarker-based detection technology. We summarize the advantages and limitations of these detection methods and discuss the challenges as well as future directions, hoping to provide new insights and references for the rapid detection of hvKp in the future. The aim of this study is to focus on the research papers related to Hypervirulent Klebsiella pneumoniae involving the period from 2012 to 2022. We conducted searches using the keywords "Hypervirulent Klebsiella pneumoniae, biomarkers, detection techniques" on ScienceDirect and Google Scholar. Additionally, we also searched on PubMed, using MeSH terms associated with the keywords (such as Klebsiella pneumoniae, Klebsiella Infections, Virulence, Biomarkers, diagnosis, etc.).
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Affiliation(s)
- Qi-Bin Zhang
- The Affiliated People's Hospital of Ningbo University, Ningbo, China
| | - Peng Zhu
- Ningbo No. 2 Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Shun Zhang
- Ningbo No. 2 Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Yan-Jing Rong
- Ningbo No. 2 Hospital, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Zuo-An Huang
- Ningbo No. 2 Hospital, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | | | - Ting Cai
- Ningbo No. 2 Hospital, Ningbo, China.
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China.
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Huang S, Dai R, Zhang Z, Zhang H, Zhang M, Li Z, Zhao K, Xiong W, Cheng S, Wang B, Wan Y. CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis. Int J Mol Sci 2023; 24:13447. [PMID: 37686249 PMCID: PMC10487896 DOI: 10.3390/ijms241713447] [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: 07/21/2023] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
CRISPR/Cas systems have found widespread applications in gene editing due to their high accuracy, high programmability, ease of use, and affordability. Benefiting from the cleavage properties (trans- or cis-) of Cas enzymes, the scope of CRISPR/Cas systems has expanded beyond gene editing and they have been utilized in various fields, particularly in live-cell imaging and bioanalysis. In this review, we summarize some fundamental working mechanisms and concepts of the CRISPR/Cas systems, describe the recent advances and design principles of CRISPR/Cas mediated techniques employed in live-cell imaging and bioanalysis, highlight the main applications in the imaging and biosensing of a wide range of molecular targets, and discuss the challenges and prospects of CRISPR/Cas systems in live-cell imaging and biosensing. By illustrating the imaging and bio-sensing processes, we hope this review will guide the best use of the CRISPR/Cas in imaging and quantifying biological and clinical elements and inspire new ideas for better tool design in live-cell imaging and bioanalysis.
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Affiliation(s)
- Shuo Huang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Rui Dai
- Institute of Oceanography, Hainan University, Haikou 570228, China;
| | - Zhiqi Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Han Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Meng Zhang
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Zhangjun Li
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Kangrui Zhao
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Wenjun Xiong
- College of Life Sciences, Hainan University, Haikou 570228, China; (S.H.); (Z.Z.); (H.Z.); (M.Z.); (Z.L.); (K.Z.); (W.X.)
| | - Siyu Cheng
- College of Art and Design, Hainan University, Haikou 570228, China;
| | - Buhua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
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Abbas N, Song S, Chang MS, Chun MS. Point-of-Care Diagnostic Devices for Detection of Escherichia coli O157:H7 Using Microfluidic Systems: A Focused Review. BIOSENSORS 2023; 13:741. [PMID: 37504139 PMCID: PMC10377133 DOI: 10.3390/bios13070741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/29/2023]
Abstract
Bacterial infections represent a serious and global threat in modern medicine; thus, it is very important to rapidly detect pathogenic bacteria, such as Escherichia coli (E. coli) O157:H7. Once treatments are delayed after the commencement of symptoms, the patient's health quickly deteriorates. Hence, real-time detection and monitoring of infectious agents are highly critical in early diagnosis for correct treatment and safeguarding public health. To detect these pathogenic bacteria, many approaches have been applied by the biosensors community, for example, widely-used polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA), culture-based method, and adenosine triphosphate (ATP) bioluminescence. However, these approaches have drawbacks, such as time-consumption, expensive equipment, and being labor-intensive, making it critical to develop ultra-sensitive and highly selective detection. The microfluidic platform based on surface plasmon resonance (SPR), electrochemical sensing, and rolling circle amplification (RCA) offers proper alternatives capable of supplementing the technological gap for pathogen detection. Note that the microfluidic biochip allows to develop rapid, sensitive, portable, and point-of-care (POC) diagnostic tools. This review focuses on recent studies regarding accurate and rapid detection of E. coli O157:H7, with an emphasis on POC methods and devices that complement microfluidic systems. We also examine the efficient whole-body detection by employing antimicrobial peptides (AMPs), which has attracted growing attention in many applications.
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Affiliation(s)
- Naseem Abbas
- Department of Mechanical Engineering, Sejong University, Gwangjin-gu, Seoul 05006, Republic of Korea
| | - Sehyeon Song
- Laboratory of Stem Cell & Neurobiology, Department of Oral Anatomy & Dental Research Institute, Seoul National University School of Dentistry, Jongno-gu, Seoul 03080, Republic of Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Natural Sciences, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Mi-Sook Chang
- Laboratory of Stem Cell & Neurobiology, Department of Oral Anatomy & Dental Research Institute, Seoul National University School of Dentistry, Jongno-gu, Seoul 03080, Republic of Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Natural Sciences, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Myung-Suk Chun
- Sensor System Research Center, Advanced Materials Research Division, Korea Institute of Science and Technology (KIST), Seongbuk-gu, Seoul 02792, Republic of Korea
- Biomedical Engineering Division, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
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Zhu L, Liang Z, Xu Y, Chen Z, Wang J, Zhou L. Ultrasensitive and Rapid Visual Detection of Escherichia coli O157:H7 Based on RAA-CRISPR/Cas12a System. BIOSENSORS 2023; 13:659. [PMID: 37367024 DOI: 10.3390/bios13060659] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
Escherichia coli (E. coli) O157:H7 is a major foodborne and waterborne pathogen that can threaten human health. Due to its high toxicity at low concentrations, it is crucial to establish a time-saving and highly sensitive in situ detection method. Herein, we developed a rapid, ultrasensitive, and visualized method for detecting E. coli O157:H7 based on a combination of Recombinase-Aided Amplification (RAA) and CRISPR/Cas12a technology. The CRISPR/Cas12a-based system was pre-amplified using the RAA method, which showed high sensitivity and enabled detecting as low as ~1 CFU/mL (fluorescence method) and 1 × 102 CFU/mL (lateral flow assay) of E. coli O157:H7, which was much lower than the detection limit of the traditional real-time PCR technology (103 CFU/mL) and ELISA (104~107 CFU/mL). In addition, we demonstrated that this method still has good applicability in practical samples by simulating the detection in real milk and drinking water samples. Importantly, our RAA-CRISPR/Cas12a detection system could complete the overall process (including extraction, amplification, and detection) within 55 min under optimized conditions, which is faster than most other reported sensors, which take several hours to several days. The signal readout could also be visualized by fluorescence generated with a handheld UV lamp or a naked-eye-detected lateral flow assay depending on the DNA reporters used. Because of the advantages of being fast, having high sensitivity, and not requiring sophisticated equipment, this method has a promising application prospect for in situ detection of trace amounts of pathogens.
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Affiliation(s)
- Lishan Zhu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Zhenda Liang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yongtao Xu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Zhiquan Chen
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiasi Wang
- Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument, School of Biomedical Engineering, Shenzhen Campus of Sun Yat-Sen University, Shenzhen 518107, China
| | - Li Zhou
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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20
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Yang H, Ledesma-Amaro R, Gao H, Ren Y, Deng R. CRISPR-based biosensors for pathogenic biosafety. Biosens Bioelectron 2023; 228:115189. [PMID: 36893718 DOI: 10.1016/j.bios.2023.115189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Pathogenic biosafety is a worldwide concern. Tools for analyzing pathogenic biosafety, that are precise, rapid and field-deployable, are highly demanded. Recently developed biotechnological tools, especially those utilizing CRISPR/Cas systems which can couple with nanotechnologies, have enormous potential to achieve point-of-care (POC) testing for pathogen infection. In this review, we first introduce the working principle of class II CRISPR/Cas system for detecting nucleic acid and non-nucleic acid biomarkers, and highlight the molecular assays that leverage CRISPR technologies for POC detection. We summarize the application of CRISPR tools in detecting pathogens, including pathogenic bacteria, viruses, fungi and parasites and their variants, and highlight the profiling of pathogens' genotypes or phenotypes, such as the viability, and drug-resistance. In addition, we discuss the challenges and opportunities of CRISPR-based biosensors in pathogenic biosafety analysis.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
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21
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Pitikultham P, Putnin T, Pimalai D, Sathirapongsasuti N, Kitiyakara C, Jiang Q, Ding B, Japrung D. Ultrasensitive Detection of MicroRNA in Human Saliva via Rolling Circle Amplification Using a DNA-Decorated Graphene Oxide Sensor. ACS OMEGA 2023; 8:15266-15275. [PMID: 37151566 PMCID: PMC10157686 DOI: 10.1021/acsomega.3c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
MicroRNAs (miRNAs) are a family of conserved small noncoding RNAs whose expression is associated with many diseases, including cancer. Salivary miRNAs are gaining popularity as noninvasive diagnostic biomarkers for cancer and other systemic disorders, but their use is limited by their low abundance and complicated detection procedure. Herein, we present a novel self-assembly approach based on rolling circle amplification (RCA) and graphene oxide (GO) for the ultrasensitive detection of miRNA21 and miRNA16 (miRNA oral cancer biomarkers in human saliva). First, target miRNA hybridizes with the RCA template. In the presence of DNA polymerase, the RCA reaction is induced and sequences matching the template are generated. Then, a nicking enzyme cuts the long ssDNA product into tiny pieces to obtain the amplified products. The DNA-decorated GO sensor was fabricated by preabsorbing the ssDNA fluorescence-labeled probe on the GO surface, resulting in fluorescence quenching. The DNA-decorated GO sensor could detect the amplified product via the self-assembly of dsDNA, leading to the desorption and recovery of the fluorescence-labeled probe. Under optimal conditions, the proposed system exhibited ultrasensitive detection; the detection limits of miRNA16 and miRNA21 were 8.81 and 3.85 fM, respectively. It showed a wide range of detection between 10 fM and 100 pM for miRNA16 and between 10 fM and 1 nM for miRNA16. It demonstrated high selectivity, distinguishing between 1- and 3-mismatch nucleotides in target miRNA. Overall, our proposed DNA-decorated GO sensor can accurately detect the salivary miRNAs and may potentially be used for the diagnosis and screening of early-stage oral cancer.
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Affiliation(s)
- Piyawat Pitikultham
- CAS
Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center
for Excellence in Nanoscience, National
Center for Nanoscience and Technology, Beijing 100190, China
- School
of Nanoscience and Technology, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Thitirat Putnin
- National
Nanotechnology Center, National Science and Technology Department
Agency, Thailand Science Park, Pathumthani 10120, Thailand
| | - Dechnarong Pimalai
- National
Nanotechnology Center, National Science and Technology Department
Agency, Thailand Science Park, Pathumthani 10120, Thailand
| | - Nuankanya Sathirapongsasuti
- Program
in Translational Medicine, Chakri Naruebodindra Medical Institute,
Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bang Pli, Samutprakarn 10540, Thailand
| | - Chagriya Kitiyakara
- Department
of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Qiao Jiang
- CAS
Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center
for Excellence in Nanoscience, National
Center for Nanoscience and Technology, Beijing 100190, China
- School
of Nanoscience and Technology, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS
Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center
for Excellence in Nanoscience, National
Center for Nanoscience and Technology, Beijing 100190, China
- School
of Nanoscience and Technology, University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Deanpen Japrung
- National
Nanotechnology Center, National Science and Technology Department
Agency, Thailand Science Park, Pathumthani 10120, Thailand
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22
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Lu B, Guo Z, Zhong K, Osire T, Sun Y, Jiang L. State of the art in CRISPR/Cas system-based signal conversion and amplification applied in the field of food analysis. Trends Food Sci Technol 2023. [DOI: 10.1016/j.tifs.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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23
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Peng X, Mei X, Yang J, Liu J, Li Y. Ultrasensitive Hybridization Chain Reaction-Assisted Multisite Exonuclease III Amplification Strategy Combined with a Direct Quantitative Fluorescence Lateral Flow Technique for Multiple Bacterial 16S rRNA Detection. Anal Chem 2023; 95:5807-5814. [PMID: 36946074 DOI: 10.1021/acs.analchem.3c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Accurate and in-time detection of bacteria conduces to preventing their rapid spread around the environment, while a nucleic acid test (NAT) is a powerful tool for early diagnosis of pathogens. Herein, we propose a hybridization chain reaction (HCR)-mediated multisite exonuclease III (Exo-III) amplification strategy (HCR/Exo-III amplifier) to achieve the one-pot and ultrasensitive isothermal amplification of bacterial 16S rRNA and a portable fluorescence detection device (PFD) to directly read signals in a lateral flow assay (LFA). In detail, the target-initiated HCR products present multiple binding sites for triggering the Exo-III amplifier that produces numerous target amplicons. Following that, the target amplicons travel up on the strip and bridge between the DNA-CdTe/CdS probes and the capture DNA to form a positive fluorescence line. After that, the strip is inserted into the PFD to accomplish the fluorescence signal reading. The constructed HCR/Exo-III amplifier-based PFD-LFA implemented the simultaneous and specific detection of three bacteria with a detection limit of a few tenths of fM for synthetic 16S rRNA fragments and dozens of CFU/mL for Staphylococcus aureus, Listeria monocytogenes, and Salmonella typhimurium in pure cultures. The sensing platform features isothermal amplification, convenient operation, and good economy, displaying great potential for on-site testing toward multiple nucleic acid analytes.
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Affiliation(s)
- Xin Peng
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Xuecui Mei
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Jiao Yang
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Jiang Liu
- School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, China
| | - Yingchun Li
- School of Science, Harbin Institute of Technology, Shenzhen 518055, China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
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24
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Liu FX, Cui JQ, Wu Z, Yao S. Recent progress in nucleic acid detection with CRISPR. LAB ON A CHIP 2023; 23:1467-1492. [PMID: 36723235 DOI: 10.1039/d2lc00928e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Recent advances in CRISPR-based biotechnologies have greatly expanded our capabilities to repurpose CRISPR for the development of molecular diagnostic systems. The key attribute that allows CRISPR to be widely utilized is its programmable and highly specific nature. In this review, we first illustrate the principle of the class 2 CRISPR nucleases for molecular diagnostics which originates from their immunologic defence systems. Next, we present the CRISPR-based schemes in the application of diagnostics with amplification-assisted or amplification-free strategies. By highlighting some of the recent advances we interpret how general bioengineering methodologies can be integrated with CRISPR. Finally, we discuss the challenges and exciting prospects for future CRISPR-based biosensing development. We hope that this review will guide the reader to systematically learn the start-of-the-art development of CRISPR-mediated nucleic acid detection and understand how to apply the CRISPR nucleases with different design concepts to more general applications in diagnostics and beyond.
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Affiliation(s)
- Frank X Liu
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Johnson Q Cui
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Zhihao Wu
- IIP-Advanced Materials, Interdisciplinary Program Office (IPO), Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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25
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Zhang J, Zhou M, Li X, Fan Y, Li J, Lu K, Wen H, Ren J. Recent advances of fluorescent sensors for bacteria detection-A review. Talanta 2023; 254:124133. [PMID: 36459871 DOI: 10.1016/j.talanta.2022.124133] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Bacterial infections have become a global public health problem. Rapid and sensitive bacterial detection is of great importance for human health. Among various sensor systems, fluorescence sensor is rapid, portable, multiplexed, and cost-efficient. Herein, we reviewed the current trends of fluorescent sensors for bacterial detection from three aspects (response materials, target and recognition way). The fluorescent materials have the advantages of high fluorescent strength, high stability, and good biocompatibility. They provide a new path for bacterial detection. Several recent fluorescent nanomaterials for bacterial detection, including semiconductor quantum dots (QDs), carbon dots (CDs), up-conversion nanoparticles (UCNPs) and metal organic frameworks (MOFs), were introduced. Their optical properties and detection mechanisms were analyzed and compared. For different response targets in the detection process, we studied the fluorescence strategy using DNA, bacteria, and metabolites as the response target. In addition, we classified the recognition way between nanomaterial and target, including specific recognition methods based on aptamers, antibodies, bacteriophages, and non-specific recognition methods based on biological functional materials. The characteristics of different recognition methods were summarized. Finally, the weaknesses and future development of bacterial fluorescence sensor were discussed. This review provides new insights into the application of fluorescent sensing systems as an important tool for bacterial detection.
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Affiliation(s)
- Jialin Zhang
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Ming Zhou
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Xin Li
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Yaqi Fan
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Jinhui Li
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Kangqiang Lu
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Herui Wen
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Jiali Ren
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Changsha, 410004, PR China.
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26
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Abavisani M, Khayami R, Hoseinzadeh M, Kodori M, Kesharwani P, Sahebkar A. CRISPR-Cas system as a promising player against bacterial infection and antibiotic resistance. Drug Resist Updat 2023; 68:100948. [PMID: 36780840 DOI: 10.1016/j.drup.2023.100948] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/25/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
The phenomenon of antibiotic resistance (AR) and its increasing global trends and destructive waves concerns patients and the healthcare system. In order to combat AR, it is necessary to explore new strategies when the current antibiotics fail to be effective. Thus, knowing the resistance mechanisms and appropriate diagnosis of bacterial infections may help enhance the sensitivity and specificity of novel strategies. On the other hand, resistance to antimicrobial compounds can spread from resistant populations to susceptible ones. Antimicrobial resistance genes (ARGs) significantly disseminate AR via horizontal and vertical gene transfer. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is a member of the bacterial immune system with the ability to remove the ARGs; therefore, it can be introduced as an effective and innovative strategy in the battle against AR. Here, we reviewed CRISPR-based bacterial diagnosis technologies. Moreover, the strategies to battle AR based on targeting bacterial chromosomes and resistance plasmids using the CRISPR-Cas system have been explained. Besides, we have presented the limitations of CRISPR delivery and potential solutions to help improve the future development of CRISPR-based platforms.
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Affiliation(s)
- Mohammad Abavisani
- Student research committee, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran; Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran
| | - Reza Khayami
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran
| | - Melika Hoseinzadeh
- Student research committee, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran
| | - Mansoor Kodori
- Non communicable Diseases Research Center, Bam University of Medical sciences, Bam, the Islamic Republic of Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India; Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Chennai, India
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran; Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, the Islamic Republic of Iran.
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27
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Sun X, Wang W, Chai Y, Zheng Z, Wang Y, Bi J, Wang Q, Hu Y, Gao Z. A DNA walker triggered isothermal amplification method based on freezing construction of AuNP probes and its application in ricin detection. Analyst 2023; 148:690-699. [PMID: 36632708 DOI: 10.1039/d2an01793h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA molecular machines are widely used in the fields of biosensors and biological detection. Among them, DNA walkers have attracted much attention due to their simple design and controllability. Herein, we attempt to develop a DNA walker triggered exponential amplification method and explore its application. The AuNP probes in the DNA walker are constructed by a freezing technology, instead of the time-consuming and complex synthesis process of the traditional method. Meanwhile, after the "recognition-cleavage-relative motion" cycle of this DNA walker reaction, the exponential amplification reaction is initiated, and leads to the fluorescence recovery of the molecular beacon. Taking ricin as a target, this new method shows a limit of detection of 2.25 pM by selecting aptamers with strong binding affinity, and exhibits a wide detection range, satisfactory specificity, and excellent stability in practical application. Therefore, our method provides a universal sensing platform and has great prospects in the fields of biosensors, food safety detection, and clinical diagnostics.
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Affiliation(s)
- Xuan Sun
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Weiya Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin 300050, China
| | - Yanyan Chai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhou Zheng
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin 300050, China
| | - Jing Bi
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Qian Wang
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Yonggang Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin 300050, China
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28
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Kumaran A, Jude Serpes N, Gupta T, James A, Sharma A, Kumar D, Nagraik R, Kumar V, Pandey S. Advancements in CRISPR-Based Biosensing for Next-Gen Point of Care Diagnostic Application. BIOSENSORS 2023; 13:202. [PMID: 36831968 PMCID: PMC9953454 DOI: 10.3390/bios13020202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 05/25/2023]
Abstract
With the move of molecular tests from diagnostic labs to on-site testing becoming more common, there is a sudden rise in demand for nucleic acid-based diagnostic tools that are selective, sensitive, flexible to terrain changes, and cost-effective to assist in point-of-care systems for large-scale screening and to be used in remote locations in cases of outbreaks and pandemics. CRISPR-based biosensors comprise a promising new approach to nucleic acid detection, which uses Cas effector proteins (Cas9, Cas12, and Cas13) as extremely specialized identification components that may be used in conjunction with a variety of readout approaches (such as fluorescence, colorimetry, potentiometry, lateral flow assay, etc.) for onsite analysis. In this review, we cover some technical aspects of integrating the CRISPR Cas system with traditional biosensing readout methods and amplification technologies such as polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA) and continue to elaborate on the prospects of the developed biosensor in the detection of some major viral and bacterial diseases. Within the scope of this article, we also discuss the recent COVID pandemic and the numerous CRISPR biosensors that have undergone development since its advent. Finally, we discuss some challenges and future prospects of CRISPR Cas systems in point-of-care testing.
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Affiliation(s)
- Akash Kumaran
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Nathan Jude Serpes
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Tisha Gupta
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Abija James
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Avinash Sharma
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Rupak Nagraik
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan 173229, Himachal Pradesh, India
| | - Vaneet Kumar
- Department of Natural Science, CT University, Ludhiana 142024, Punjab, India
| | - Sadanand Pandey
- Department of Chemistry, College of Natural Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea
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29
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Liu J, Xie G, Lv S, Xiong Q, Xu H. Recent applications of rolling circle amplification in biosensors and DNA nanotechnology. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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30
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Fang T, Shen J, Xue J, Jiang Y, Guo D, Yang J, Kong X, Xu X, Wang X. Sensitive and Rapid Detection of Escherichia coli O157:H7 From Beef Samples Based on Recombinase Aided Amplification Assisted CRISPR/Cas12a System. J AOAC Int 2022; 106:156-164. [PMID: 36005831 DOI: 10.1093/jaoacint/qsac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Escherichia coli O157:H7, being the cause of hemorrhagic colitis in humans, is recognized as one of the most dangerous and widespread foodborne pathogens. A highly specific, sensitive, and rapid E. coli O157:H7 detection method needs to be developed since the traditional detection methods are complex, costly, and time-consuming. OBJECTIVE In this study, a recombinase aided amplification (RAA) assisted CRISPR/Cas12a (RAA-CRISPR/Cas12a) fluorescence platform for specific, sensitive, and rapid nucleic acid detection of E. coli O157:H7 was introduced. METHODS First, the feasibility (components of CRISPR/Cas12a system) of the developed method was evaluated. Then a total of 34 bacterial strains were used for the specificity test, and gradient dilutions of extracted DNA and bacterial solutions of E. coli O157:H7 were prepared for the sensitivity test. Third, a real-time PCR assay for detection of the specific wzy gene of E. coli O157:H7 (FDA's Bacteriological Analytical Manual) was used for sensitivity comparison. Finally, analysis of RAA-CRISPR/Cas12a detection in spiked and 93 real ground beef samples was carried out. RESULTS The developed RAA-CRISPR/Cas12a method showed high specificity, and the detection could be completed within 30 min (after 4 h enrichment in spiked ground beef samples). The limit of detection (LOD) of bacterial concentrations and genomic DNA was 5.4 × 102 CFU/mL and 7.5 × 10-4 ng/μL, respectively, which exhibited higher sensitivity than the RAA-gel electrophoresis and RT-PCR methods. Furthermore, it was shown that E. coli O157:H7 in ground beef samples could be positively detected after 4 h enrichment when the initial bacterial inoculum was 9.0 CFU/25 g. The detection results of the RAA-CRISPR/Cas12a method were 100% consistent with those of the RT-PCR and traditional culture-based methods while screening the E. coli O157:H7 from 93 local collected ground beef samples. CONCLUSIONS The developed RAA-CRISPR/Cas12a method showed high specificity, high sensitivity, and rapid positive detection of E. coli O157:H7 from ground beef samples. HIGHLIGHTS The RAA-CRISPR/Cas12a system proposed in this study provided an alternative molecular tool for quick, specific, sensitive, and accurate detection of E. coli O157:H7 in foods.
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Affiliation(s)
- Taisong Fang
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Jinling Shen
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Junxin Xue
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Yuan Jiang
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Dehua Guo
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Jielin Yang
- Technology Center for Animal Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai 200135, China
| | - Xiangxiang Kong
- Shanghai University, School of Life Sciences, Shanghai 200444, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Xiang Wang
- University of Shanghai for Science and Technology, School of Health Science and Engineering, Shanghai 400715, China
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31
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Lu Y, Yang H, Bai J, He Q, Deng R. CRISPR-Cas based molecular diagnostics for foodborne pathogens. Crit Rev Food Sci Nutr 2022; 64:5269-5289. [PMID: 36476134 DOI: 10.1080/10408398.2022.2153792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Foodborne pathogenic infection has brought multifaceted issues to human life, leading to an urgent demand for advanced detection technologies. CRISPR/Cas-based biosensors have the potential to address various challenges that exist in conventional assays such as insensitivity, long turnaround time and complex pretreatments. In this perspective, we review the relevant strategies of CRISPR/Cas-assisted diagnostics on foodborne pathogens, focusing on biosensing platforms for foodborne pathogens based on fluorescence, colorimetric, (electro)chemiluminescence, electrochemical, and surface-enhanced Raman scattering detection. It summarizes their detection principles by the clarification of foodborne pathogenic bacteria, fungi, and viruses. Finally, we discuss the current challenges or technical barriers of these methods against broad application, and put forward alternative solutions to improve CRISPR/Cas potential for food safety.
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Affiliation(s)
- Yunhao Lu
- College of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
| | - Jinrong Bai
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, P.R. China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, P.R. China
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32
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Kundar R, Gokarn K. CRISPR-Cas System: A Tool to Eliminate Drug-Resistant Gram-Negative Bacteria. Pharmaceuticals (Basel) 2022; 15:ph15121498. [PMID: 36558949 PMCID: PMC9781512 DOI: 10.3390/ph15121498] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
Rapidly emerging drug-resistant superbugs, especially Gram-negative bacteria, pose a serious threat to healthcare systems all over the globe. Newer strategies are being developed to detect and overcome the arsenal of weapons that these bacteria possess. The development of antibiotics is time-consuming and may not provide full proof of action on evolving drug-resistant pathogens. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are promising in curbing drug-resistant bacteria. This review focuses on the pathogenesis of Gram-negative bacteria, emergence of antimicrobial drug resistance, and their treatment failures. It also draws attention to the present status of the CRISPR-Cas system in diagnosisand treatment of Gram-negative bacterial infections.
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Affiliation(s)
- Rajeshwari Kundar
- Department of Microbiology, Sir H.N. Medical Research Society, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai 400004, Maharashtra, India
| | - Karuna Gokarn
- Department of Microbiology, Sir H.N. Medical Research Society, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai 400004, Maharashtra, India
- Department of Microbiology, St. Xavier’s College, 5- Mahapalika Marg, Mumbai 400001, Maharashtra, India
- Correspondence: or
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Chakraborty J, Chaudhary AA, Khan SUD, Rudayni HA, Rahaman SM, Sarkar H. CRISPR/Cas-Based Biosensor As a New Age Detection Method for Pathogenic Bacteria. ACS OMEGA 2022; 7:39562-39573. [PMID: 36385843 PMCID: PMC9648122 DOI: 10.1021/acsomega.2c04513] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/03/2022] [Indexed: 05/25/2023]
Abstract
Methods enabling rapid and on-site detection of pathogenic bacteria are a prerequisite for public health assurance, medical diagnostics, ensuring food safety and security, and research. Many current bacteria detection technologies are inconvenient and time-consuming, making them unsuitable for field detection. New technology based on the CRISPR/Cas system has the potential to fill the existing gaps in detection. The clustered regularly interspaced short palindromic repeats (CRISPR) system is a part of the bacterial adaptive immune system to protect them from intruding bacteriophages. The immunological memory is saved by the CRISPR array of bacteria in the form of short DNA sequences (spacers) from invading viruses and incorporated with the CRISPR DNA repeats. Cas proteins are responsible for triggering and initiating the adaptive immune function of CRISPR/Cas systems. In advanced biological research, the CRISPR/Cas system has emerged as a significant tool from genome editing to pathogen detection. By considering its sensitivity and specificity, this system can become one of the leading detection methods for targeting DNA/RNA. This technique is well applied in virus detection like Dengue, ZIKA, SARS-CoV-2, etc., but for bacterial detection, this CRISPR/Cas system is limited to only a few organisms to date. In this review, we have discussed the different techniques based on the CRISPR/Cas system that have been developed for the detection of various pathogenic bacteria like L. monocytogenes, M. tuberculosis, Methicillin-resistant S. aureus, Salmonella, E. coli, P. aeruginosa, and A. baumannii.
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Affiliation(s)
- Joydeep Chakraborty
- Department
of Microbiology, Raiganj University, Raiganj, West Bengal733134, India
| | - Anis Ahmad Chaudhary
- Department
of Biology, College of Science, Imam Mohammad
Ibn Saud Islamic University (IMSIU), Riyadh11623, Saudi
Arabia
| | - Salah-Ud-Din Khan
- Department
of Biochemistry, College of Medicine, Imam
Mohammad Ibn Saud Islamic University (IMSIU), Riyadh11623, Saudi
Arabia
| | - Hassan Ahmad Rudayni
- Department
of Biology, College of Science, Imam Mohammad
Ibn Saud Islamic University (IMSIU), Riyadh11623, Saudi
Arabia
| | | | - Hironmoy Sarkar
- Department
of Microbiology, Raiganj University, Raiganj, West Bengal733134, India
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Li Y, Gao Y, Ling N, Shen Y, Zhang D, Ou D, Zhang X, Jiao R, Zhu C, Ye Y. Rapid and simple quantitative identification of Listeria monocytogenes in cheese by isothermal sequence exchange amplification based on surface-enhanced Raman spectroscopy. J Dairy Sci 2022; 105:9450-9462. [DOI: 10.3168/jds.2022-22181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022]
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35
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Yuan B, Yuan C, Li L, Long M, Chen Z. Application of the CRISPR/Cas System in Pathogen Detection: A Review. Molecules 2022; 27:molecules27206999. [PMID: 36296588 PMCID: PMC9610700 DOI: 10.3390/molecules27206999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 11/18/2022] Open
Abstract
Early and rapid diagnosis of pathogens is important for the prevention and control of epidemic disease. The polymerase chain reaction (PCR) technique requires expensive instrument control, a special test site, complex solution treatment steps and professional operation, which can limit its application in practice. The pathogen detection method based on the clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated protein (CRISPR/Cas) system is characterized by strong specificity, high sensitivity and convenience for detection, which is more suitable for practical applications. This article first reviews the CRISPR/Cas system, and then introduces the application of the two types of systems represented by Type II (cas9), Type V (cas12a, cas12b, cas14a) and Type VI (cas13a) in pathogen detection. Finally, challenges and prospects are proposed.
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36
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Li J, Wang Y, Wang B, Lou J, Ni P, Jin Y, Chen S, Duan G, Zhang R. Application of CRISPR/Cas Systems in the Nucleic Acid Detection of Infectious Diseases. Diagnostics (Basel) 2022; 12:diagnostics12102455. [PMID: 36292145 PMCID: PMC9600689 DOI: 10.3390/diagnostics12102455] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
The CRISPR/Cas system is a protective adaptive immune system against attacks from foreign mobile genetic elements. Since the discovery of the excellent target-specific sequence recognition ability of the CRISPR/Cas system, the CRISPR/Cas system has shown excellent performance in the development of pathogen nucleic-acid-detection technology. In combination with various biosensing technologies, researchers have made many rapid, convenient, and feasible innovations in pathogen nucleic-acid-detection technology. With an in-depth understanding and development of the CRISPR/Cas system, it is no longer limited to CRISPR/Cas9, CRISPR/Cas12, and other systems that had been widely used in the past; other CRISPR/Cas families are designed for nucleic acid detection. We summarized the application of CRISPR/Cas-related technology in infectious-disease detection and its development in SARS-CoV-2 detection.
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Affiliation(s)
- Junwei Li
- International School of Public Health and One Health, First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yuexia Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Juan Lou
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Peng Ni
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Rongguang Zhang
- International School of Public Health and One Health, First Affiliated Hospital of Hainan Medical University, Haikou 570102, China
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Correspondence:
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37
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Liu J, Wu D, Chen J, Jia S, Chen J, Wu Y, Li G. CRISPR-Cas systems mediated biosensing and applications in food safety detection. Crit Rev Food Sci Nutr 2022; 64:2960-2985. [PMID: 36218189 DOI: 10.1080/10408398.2022.2128300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Food safety, closely related to economic development of food industry and public health, has become a global concern and gained increasing attention worldwide. Effective detection technology is of great importance to guarantee food safety. Although several classical detection methods have been developed, they have some limitations in portability, selectivity, and sensitivity. The emerging CRISPR-Cas systems, uniquely integrating target recognition specificity, signal transduction, and efficient signal amplification abilities, possess superior specificity and sensitivity, showing huge potential to address aforementioned challenges and develop next-generation techniques for food safety detection. In this review, we focus on recent progress of CRISPR-Cas mediated biosensing and their applications in food safety monitoring. The properties and principles of commonly used CRISPR-Cas systems are highlighted. Notably, the frequently coupled nucleic acid amplification strategies to enhance their selectivity and sensitivity, especially isothermal amplification methods, as well as various signal output modes are also systematically summarized. Meanwhile, the application of CRISPR-Cas systems-based biosensors in food safety detection including foodborne virus, foodborne bacteria, food fraud, genetically modified organisms (GMOs), toxins, heavy metal ions, antibiotic residues, and pesticide residues is comprehensively described. Furthermore, the current challenges and future prospects in this field are tentatively discussed.
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Affiliation(s)
- Jianghua Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Jiahui Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Shijie Jia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Jian Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
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38
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Zhang X, Shi Y, Chen G, Wu D, Wu Y, Li G. CRISPR/Cas Systems-Inspired Nano/Biosensors for Detecting Infectious Viruses and Pathogenic Bacteria. SMALL METHODS 2022; 6:e2200794. [PMID: 36114150 DOI: 10.1002/smtd.202200794] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Infectious pathogens cause severe human illnesses and great deaths per year worldwide. Rapid, sensitive, and accurate detection of pathogens is of great importance for preventing infectious diseases caused by pathogens and optimizing medical healthcare systems. Inspired by a microbial defense system (i.e., CRISPR/ CRISPR-associated proteins (Cas) system, an adaptive immune system for protecting microorganisms from being attacked by invading species), a great many new biosensors have been successfully developed and widely applied in the detection of infectious viruses and pathogenic bacteria. Moreover, advanced nanotechnologies have also been integrated into these biosensors to improve their detection stability, sensitivity, and accuracy. In this review, the recent advance in CRISPR/Cas systems-based nano/biosensors and their applications in the detection of infectious viruses and pathogenic bacteria are comprehensively reviewed. First of all, the categories and working principles of CRISPR/Cas systems for establishing the nano/biosensors are simply introduced. Then, the design and construction of CRISPR/Cas systems-based nano/biosensors are comprehensively discussed. In the end, attentions are focused on the applications of CRISPR/Cas systems-based nano/biosensors in the detection of infectious viruses and pathogenic bacteria. Impressively, the remaining opportunities and challenges for the further design and development of CRISPR/Cas system-based nano/biosensors and their promising applications are proposed.
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Affiliation(s)
- Xianlong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Yiheng Shi
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Guang Chen
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Di Wu
- Institute for Global Food Security, Queen's University Belfast, Belfast, BT95DL, UK
| | - Yongning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, 100021, P. R. China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
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39
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Huang T, Zhang R, Li J. CRISPR-Cas-based techniques for pathogen detection: Retrospect, recent advances, and future perspectives. J Adv Res 2022:S2090-1232(22)00240-5. [PMID: 36367481 PMCID: PMC10403697 DOI: 10.1016/j.jare.2022.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/16/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Early detection of pathogen-associated diseases are critical for effective treatment. Rapid, specific, sensitive, and cost-effective diagnostic technologies continue to be challenging to develop. The current gold standard for pathogen detection, polymerase chain reaction technology, has limitations such as long operational cycles, high cost, and high technician and instrumentation requirements. AIM OF REVIEW This review examines and highlights the technical advancements of CRISPR-Cas in pathogen detection and provides an outlook for future development, multi-application scenarios, and clinical translation. KEY SCIENTIFIC CONCEPTS OF REVIEW Approaches enabling clinical detection of pathogen nucleic acids that are highly sensitive, specific, cheap, and portable are necessary. CRISPR-Cas9 specificity in targeting nucleic acids and "collateral cleavage" activity of CRISPR-Cas12/Cas13/Cas14 show significant promise in nucleic acid detection technology. These methods have a high specificity, versatility, and rapid detection cycle. In this paper, CRISPR-Cas-based detection methods are discussed in depth. Although CRISPR-Cas-mediated pathogen diagnostic solutions face challenges, their powerful capabilities will pave the way for ideal diagnostic tools.
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40
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Huang Z, Liu S, Pei X, Li S, He Y, Tong Y, Liu G. Fluorescence Signal-Readout of CRISPR/Cas Biosensors for Nucleic Acid Detection. BIOSENSORS 2022; 12:bios12100779. [PMID: 36290917 PMCID: PMC9599699 DOI: 10.3390/bios12100779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/27/2022] [Accepted: 09/07/2022] [Indexed: 05/25/2023]
Abstract
The CRISPR/Cas system is now being used extensively in nucleic acid detection applications, particularly after the trans-cleavage activity of several Cas effectors was found. A CRISPR/Cas system combined with multiple signal-readout techniques has been developed for various molecular diagnostics applications. Fluorescence is now a widely utilized dominant read-out technique in CRISPR biosensors. An in-depth understanding of various fluorescence readout types and variables affecting the fluorescence signals can facilitate better experimental designs to effectively improve the analytical performance. There are the following two commonly used types of CRISPR/Cas detection modes: the first is based on binding activity, such as Cas9 and dCas9; the second is based on cleavage activity, such as Cas12a, Cas12b, Cas13, and Cas14. In this review, fluorescence signal-readout strategies from the last 5 years based on the binding activity and cleavage activity of the CRISPR/Cas system with fundamentals and examples are fully discussed. A detailed comparison of the available fluorescent reporter sequences and design principles is summarized. Current challenges and further applications of CRISPR-based detection methods will be discussed according to the most recent developments.
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Affiliation(s)
- Zhaohe Huang
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Sitong Liu
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Xiaojing Pei
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Shujing Li
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Yifan He
- Institute of Cosmetic Regulatory Science and College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100048, China
| | - Yigang Tong
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing 100029, China
| | - Guoqi Liu
- Biotecnovo (Beijing) Co., Ltd., Beijing Economic and Technological Development Zone, Beijing 100176, China
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41
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A novel fluorescence biosensor based on double-stranded DNA branch migration-induced HCR and DNAzyme feedback circuit for sensitive detection of Pseudomonas aeruginosa (clean version). Anal Chim Acta 2022; 1232:340449. [DOI: 10.1016/j.aca.2022.340449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/18/2022] [Accepted: 09/25/2022] [Indexed: 12/30/2022]
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42
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Wang H, Jia C, Li H, Yin R, Chen J, Li Y, Yue M. Paving the way for precise diagnostics of antimicrobial resistant bacteria. Front Mol Biosci 2022; 9:976705. [PMID: 36032670 PMCID: PMC9413203 DOI: 10.3389/fmolb.2022.976705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/19/2022] [Indexed: 12/26/2022] Open
Abstract
The antimicrobial resistance (AMR) crisis from bacterial pathogens is frequently emerging and rapidly disseminated during the sustained antimicrobial exposure in human-dominated communities, posing a compelling threat as one of the biggest challenges in humans. The frequent incidences of some common but untreatable infections unfold the public health catastrophe that antimicrobial-resistant pathogens have outpaced the available countermeasures, now explicitly amplified during the COVID-19 pandemic. Nowadays, biotechnology and machine learning advancements help create more fundamental knowledge of distinct spatiotemporal dynamics in AMR bacterial adaptation and evolutionary processes. Integrated with reliable diagnostic tools and powerful analytic approaches, a collaborative and systematic surveillance platform with high accuracy and predictability should be established and implemented, which is not just for an effective controlling strategy on AMR but also for protecting the longevity of valuable antimicrobials currently and in the future.
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Affiliation(s)
- Hao Wang
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Chenhao Jia
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Hongzhao Li
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Rui Yin
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Jiang Chen
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
| | - Yan Li
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
| | - Min Yue
- Institute of Preventive Veterinary Sciences & Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jiang Chen, ; Yan Li, ; Min Yue,
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Li Y, Man S, Ye S, Liu G, Ma L. CRISPR-Cas-based detection for food safety problems: Current status, challenges, and opportunities. Compr Rev Food Sci Food Saf 2022; 21:3770-3798. [PMID: 35796408 DOI: 10.1111/1541-4337.13000] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022]
Abstract
Food safety is one of the biggest public issues occurring around the world. Microbiological, chemical, and physical hazards can lead to food safety issues, which may occur at all stages of the supply chain. In order to tackle food safety issues and safeguard consumer health, rapid, accurate, specific, and field-deployable detection methods meeting diverse requirements are one of the imperative measures for food safety assurance. CRISPR-Cas system, a newly emerging technology, has been successfully repurposed in biosensing and has demonstrated huge potential to establish conceptually novel detection methods with high sensitivity and specificity. This review focuses on CRISPR-Cas-based detection and its current status and huge potential specifically for food safety inspection. We firstly illustrate the pending problems in food safety and summarize the popular detection methods. We then describe the potential applications of CRISPR-Cas-based detection in food safety inspection. Finally, the challenges and futuristic opportunities are proposed and discussed. Generally speaking, the current food safety detection methods are still unsatisfactory in some ways such as being time-consuming, displaying unmet sensitivity and specificity standards, and there is a comparative paucity of multiplexed testing and POCT. Recent studies have shown that CRISPR-Cas-based biosensing is an innovative and fast-expanding technology, which could make up for the shortcomings of the existing methods or even replace them. To sum up, the implementation of CRISPR-Cas and the integration of CRISPR-Cas with other techniques is promising and desirable, which is expected to provide "customized" and "smart" detection methods for food safety inspection in the coming future.
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Affiliation(s)
- 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
| | - 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
| | - Guozhen Liu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 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
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44
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Xia J, Bu T, Jia P, He K, Wang X, Sun X, Wang L. Polydopamine nanospheres-assisted direct PCR for rapid detection of Escherichia coli O157:H7. Anal Biochem 2022; 654:114797. [DOI: 10.1016/j.ab.2022.114797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/22/2022] [Indexed: 11/01/2022]
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45
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Selvam K, Ahmad Najib M, Khalid MF, Ozsoz M, Aziah I. CRISPR-Cas Systems-Based Bacterial Detection: A Scoping Review. Diagnostics (Basel) 2022; 12:diagnostics12061335. [PMID: 35741144 PMCID: PMC9221980 DOI: 10.3390/diagnostics12061335] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
Recently, CRISPR-Cas system-based assays for bacterial detection have been developed. The aim of this scoping review is to map existing evidence on the utilization of CRISPR-Cas systems in the development of bacterial detection assays. A literature search was conducted using three databases (PubMed, Scopus, and Cochrane Library) and manual searches through the references of identified full texts based on a PROSPERO-registered protocol (CRD42021289140). Studies on bacterial detection using CRISPR-Cas systems that were published before October 2021 were retrieved. The Critical Appraisal Skills Programme (CASP) qualitative checklist was used to assess the risk of bias for all the included studies. Of the 420 studies identified throughout the search, 46 studies that met the inclusion criteria were included in the final analysis. Bacteria from 17 genera were identified utilising CRISPR-Cas systems. Most of the bacteria came from genera such as Staphylococcus, Escherichia, Salmonella, Listeria, Mycobacterium and Streptococcus. Cas12a (64%) is the most often used Cas enzyme in bacterial detection, followed by Cas13a (13%), and Cas9 (11%). To improve the signal of detection, 83% of the research exploited Cas enzymes’ trans-cleavage capabilities to cut tagged reporter probes non-specifically. Most studies used the extraction procedure, whereas only 17% did not. In terms of amplification methods, isothermal reactions were employed in 66% of the studies, followed by PCR (23%). Fluorescence detection (67%) was discovered to be the most commonly used method, while lateral flow biosensors (13%), electrochemical biosensors (11%), and others (9%) were found to be less commonly used. Most of the studies (39) used specific bacterial nucleic acid sequences as a target, while seven used non-nucleic acid targets, including aptamers and antibodies particular to the bacteria under investigation. The turnaround time of the 46 studies was 30 min to 4 h. The limit of detection (LoD) was evaluated in three types of concentration, which include copies per mL, CFU per mL and molarity. Most of the studies used spiked samples (78%) rather than clinical samples (22%) to determine LoD. This review identified the gap in clinical accuracy evaluation of the CRISPR-Cas system in bacterial detection. More research is needed to assess the diagnostic sensitivity and specificity of amplification-free CRISPR-Cas systems in bacterial detection for nucleic acid-based tests.
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Affiliation(s)
- Kasturi Selvam
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
| | - Mohamad Ahmad Najib
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
| | - Muhammad Fazli Khalid
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
| | - Mehmet Ozsoz
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
- Department of Biomedical Engineering, Near East University, Nicosia 99138, Turkey
| | - Ismail Aziah
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.); (M.O.)
- Correspondence:
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He D, Liu G, Yang J, Jiang X, Wang H, Fan Y, Gong S, Wei F, Diao Y, Tang Y. Specific High-Sensitivity Enzymatic Molecular Detection System Termed RPA-Based CRISPR-Cas13a for Duck Tembusu Virus Diagnostics. Bioconjug Chem 2022; 33:1232-1240. [PMID: 35586918 DOI: 10.1021/acs.bioconjchem.2c00200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In China, drastic losses in the economy have been caused by the Tembusu virus (TMUV), the causative agent of the egg-drop syndrome, to the duck-raising industry. To succeed in preventing and controlling infections, extant techniques must be upgraded to achieve fast detection of viruses. This work is the first attempt to present the development of a recombinase polymerase amplification (RPA)-based clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas13a approach for the TMUV infection diagnosis, where the CRISPR-Cas13a system is exploited, i.e., the programmability of CRISPR RNA (crRNA) and the promiscuous RNase collateral cleavage of Cas13a upon recognition of target RNAs. A prokaryotic expression system was utilized for the expression of LwCas13a soluble protein, while its purification was accomplished by nickel-nitrilotriacetic acid (Ni-NTA) agarose. In the design of a particular crRNA, the target used was the TMUV NS3 RNA transcribed in vitro. The signals used for the Cas13a activity validation were an RNA-bound fluorescent group (single-stranded) and a quenching fluorophore. In the present work, a specific high-sensitivity enzymatic molecular detection system termed RPA-based CRISPR-Cas13a was established by combining Cas13a with T7 transcription and RPA for sensitive detection of TMUV at room temperature. This system can detect 102 copies of the target TMUV DNA standard/μL within 50 min. A comparison revealed that the specificity was superior to that for other avian viruses. Furthermore, the RPA-based CRISPR-Cas13a detection system was successfully applied for clinical samples, and its performance is comparable to the reverse-transcriptase real-time quantitative polymerase chain reaction (RT-qPCR). Being satisfyingly reliable, simple, specific, and sensitive, our RPA-based CRISPR-Cas13a detection system could be expanded and universalized for identifying other viruses, enabling quick detection in the field with a portable lateral flow dipstick.
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Affiliation(s)
- Dalin He
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Gang Liu
- Shandong Provincial Animal Husbandry General Station, Jinan 250102, China
| | - Jing Yang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Xiaoning Jiang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Hongzhi Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Yaru Fan
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Shangyu Gong
- Jinzhou Agricultural and Rural Comprehensive Service Center, Jinzhou 121000, China
| | - Feng Wei
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an 271018, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an 271018, China
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Habimana JDD, Huang R, Muhoza B, Kalisa YN, Han X, Deng W, Li Z. Mechanistic insights of CRISPR/Cas nucleases for programmable targeting and early-stage diagnosis: A review. Biosens Bioelectron 2022; 203:114033. [DOI: 10.1016/j.bios.2022.114033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/21/2022]
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Bhattacharjee R, Nandi A, Mitra P, Saha K, Patel P, Jha E, Panda PK, Singh SK, Dutt A, Mishra YK, Verma SK, Suar M. Theragnostic application of nanoparticle and CRISPR against food-borne multi-drug resistant pathogens. Mater Today Bio 2022; 15:100291. [PMID: 35711292 PMCID: PMC9194658 DOI: 10.1016/j.mtbio.2022.100291] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/25/2022] Open
Abstract
Foodborne infection is one of the leading sources of infections spreading across the world. Foodborne pathogens are recognized as multidrug-resistant (MDR) pathogens posing a significant problem in the food industry and healthy consumers resulting in enhanced economic burden, and nosocomial infections. The continued search for enhanced microbial detection tools has piqued the interest of the CRISPR-Cas system and Nanoparticles. CRISPR-Cas system is present in the bacterial genome of some prokaryotes and is repurposed as a theragnostic tool against MDR pathogens. Nanoparticles and composites have also emerged as an efficient tool in theragnostic applications against MDR pathogens. The diagnostic limitations of the CRISPR-Cas system are believed to be overcome by a synergistic combination of the nanoparticles system and CRISPR-Cas using nanoparticles as vehicles. In this review, we have discussed the diagnostic application of CRISPR-Cas technologies along with their potential usage in applications like phage resistance, phage vaccination, strain typing, genome editing, and antimicrobial. we have also elucidated the antimicrobial and detection role of nanoparticles against foodborne MDR pathogens. Moreover, the novel combinatorial approach of CRISPR-Cas and nanoparticles for their synergistic effects in pathogen clearance and drug delivery vehicles has also been discussed. Bacterial CRISPR Cas system are repurposed as a thergodiganostic tool against MDR pathogen. Combinatorial approach of CRISPR-Cas and Nanoparticle is used as delivery vehicle and clearing pathogens. CRISPR-Cas and Nanoparticles is a tool for the food safety profiling of MDR food-borne pathogen.
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Affiliation(s)
- Rahul Bhattacharjee
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Aditya Nandi
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Priya Mitra
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Koustav Saha
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Paritosh Patel
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Ealisha Jha
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
- Corresponding author.
| | - Sushil Kumar Singh
- DBT- NECAB, Department of Agricultural Biotechnology, Assam Agriculture University, Jorhat, 785013, Assam, India
| | - Ateet Dutt
- Instituto de Investigaciones en Materiales, UNAM, CDMX, Mexico
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alsion 2, DK-6400, Sønderborg, Denmark
- Corresponding author.
| | - Suresh K. Verma
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
- Corresponding author. KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India.
| | - Mrutyunjay Suar
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
- Corresponding author.
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Shin J, Miller M, Wang YC. Recent advances in CRISPR-based systems for the detection of foodborne pathogens. Compr Rev Food Sci Food Saf 2022; 21:3010-3029. [PMID: 35483732 DOI: 10.1111/1541-4337.12956] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/13/2022]
Abstract
There has long been a need for more advanced forms of pathogen detection in the food industry. Though in its infancy, biosensing based on clustered regularly interspaced short palindromic repeats (CRISPR) has the potential to solve many problems that cannot be addressed using conventional methods. In this review, we briefly introduce and classify the various CRISPR/Cas protein effectors that have thus far been used in biosensors. We then assess the current state of CRISPR technology in food-safety contexts; describe how each Cas effector is utilized in foodborne-pathogen detection; and discuss the limitations of the current technology, as well as how it might usefully be applied in other areas of the food industry. We conclude that, if the limitations of existing CRISPR/Cas-based detection methods are overcome, they can be deployed on a wide scale and produce a range of positive food-safety outcomes.
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Affiliation(s)
- Jiyong Shin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Michael Miller
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yi-Cheng Wang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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