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Liu Y, Shi Y, Wang S, Liu S, Shang M, Zhao B, Liu H, Yang C, Wang F, Kwok CK, Wang H. Hook-Like DNAzyme-Activated Autocatalytic Biosensor for the Universal Detection of Pathogenic Bacteria. Anal Chem 2024; 96:11951-11958. [PMID: 38990770 DOI: 10.1021/acs.analchem.4c01757] [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: 07/13/2024]
Abstract
DNAzyme-based assays have found extensive utility in pathogenic bacteria detection but often suffer from limited sensitivity and specificity. The integration of a signal amplification strategy could address this challenge, while the existing combination methods require extensive modification to accommodate various DNAzymes, limiting the wide-spectrum bacteria detection. We introduced a novel hook-like DNAzyme-activated autocatalytic nucleic acid circuit for universal pathogenic bacteria detection. The hook-like connector DNA was employed to seamlessly integrate the recognition element DNAzyme with the isothermal enzyme-free autocatalytic hybridization chain reaction and catalytic hairpin assembly for robust exponential signal amplification. This innovative autocatalytic circuit substantially amplifies the output signals from the DNAzyme recognition module, effectively overcoming DNAzyme's inherent sensitivity constraints in pathogen identification. The biosensor exhibits a strong linear response within a range of 1.5 × 103 to 3.7 × 107 CFU/mL, achieving a detection limit of 1.3 × 103 CFU/mL. Noted that the sensor's adaptability as a universal detection platform is established by simply modifying the hook-like connector module, enabling the detection of various pathogenic bacteria of considerable public health importance reported by the World Health Organization, including Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, and Salmonella typhimurium. Additionally, the specificity of DNAzyme in bacterial detection is markedly improved due to the signal amplification process of the autocatalytic circuit. This hook-like DNAzyme-activated autocatalytic platform presents a versatile, sensitive, and specific approach for pathogenic bacteria detection, promising to significantly expand the applications of DNAzyme in bacteria detection.
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Affiliation(s)
- Yaqi Liu
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Yulong Shi
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Siyuan Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Sijia Liu
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Min Shang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Bingyue Zhao
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Hanghang Liu
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Changying Yang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430000, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong ,Hong Kong SAR 999077, China
| | - Huimin Wang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei 443002, China
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2
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Yang Y, Xue H, Tang Y, Tao W, Wang Y, Guan M, Fei Y, Wang S, Wang L, Xiong X. Development of a one-pot and sequence-specific LAMP assay based on the self-quenching probe integrated by the complementary oligonucleotide for an enhanced fluorescence quenching. Food Chem 2024; 441:138354. [PMID: 38183726 DOI: 10.1016/j.foodchem.2024.138354] [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: 10/13/2023] [Revised: 12/25/2023] [Accepted: 01/01/2024] [Indexed: 01/08/2024]
Abstract
Single-modified fluorogenic primer (Sfp) enables accurate identification of LAMP amplicons without being affected by non-specific products. However, the fluorescence self-quenching by nucleobases for Sfp is generally of low efficiency, and the high background signal makes it a great challenge to achieve visual inspection with naked eyes. In the present study, the oligonucleotide (Ao) complementary to Sfp was designed, which would hybridize to Sfp and dramatically heighten the quenching effect, leading to a low background signal in negative reaction. Instead, for positive reaction, Sfp is incorporated into the double-stranded amplicons, resulting in dequenching and consequently, enhanced fluorescence. The detection scheme can be further improved by a dual-color fluorescence strategy, allowing visual detection of 1 pg rainbow trout DNA in a closed-tube format within 30 min. Therefore, our LAMP-Ao-Sfp assay represents a useful tool for rapid and sensitive detection, and can serve as a reliable method for on-site detection in low-resource settings.
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Affiliation(s)
- Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Yalin Tang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Wenjia Tao
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yaru Wang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Mingyue Guan
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yanjin Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Shihui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Libin Wang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China.
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3
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Yadav PK, Singh S, Paul M, Kumar S, Ponmariappan S, Thavaselvam D. Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices. Ann Clin Microbiol Antimicrob 2024; 23:30. [PMID: 38600514 PMCID: PMC11007888 DOI: 10.1186/s12941-024-00693-4] [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: 06/05/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Melioidosis, caused by the category B biothreat agent Burkholderia pseudomallei, is a disease with a high mortality rate and requires an immediate culture-independent diagnosis for effective disease management. In this study, we developed a highly sensitive qPCR assay for specific detection of Burkholderia pseudomallei and melioidosis disease diagnosis based on a novel target sequence. METHODS An extensive in-silico analysis was done to identify a novel and highly conserved sequence for developing a qPCR assay. The specificity of the developed assay was analyzed with 65 different bacterial cultures, and the analytical sensitivity of the assay was determined with the purified genomic DNA of B. pseudomallei. The applicability of the assay for B. pseudomallei detection in clinical and environmental matrices was evaluated by spiking B. pseudomallei cells in the blood, urine, soil, and water along with suitable internal controls. RESULTS A novel 85-nucleotide-long sequence was identified using in-silico tools and employed for the development of the highly sensitive and specific quantitative real-time PCR assay S664. The assay S664 was found to be highly specific when evaluated with 65 different bacterial cultures related and non-related to B. pseudomallei. The assay was found to be highly sensitive, with a detection limit of 3 B. pseudomallei genome equivalent copies per qPCR reaction. The detection limit in clinical matrices was found to be 5 × 102 CFU/mL for both human blood and urine. In environmental matrices, the detection limit was found to be 5 × 101 CFU/mL of river water and 2 × 103 CFU/gm of paddy field soil. CONCLUSIONS The findings of the present study suggest that the developed assay S664 along with suitable internal controls has a huge diagnostic potential and can be successfully employed for specific, sensitive, and rapid molecular detection of B. pseudomallei in various clinical and environmental matrices.
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Affiliation(s)
- Pranjal Kumar Yadav
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Suchetna Singh
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Moumita Paul
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Sanjay Kumar
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India.
| | - S Ponmariappan
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Duraipandian Thavaselvam
- O/o DGLS, Defence Research and Development Organization, Ministry of Defence, SSPL Campus, Timarpur, New Delhi, 110 054, India.
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4
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Li C, Liu C, Liu R, Wang Y, Li A, Tian S, Cheng W, Ding S, Li W, Zhao M, Xia Q. A novel CRISPR/Cas14a-based electrochemical biosensor for ultrasensitive detection of Burkholderia pseudomallei with PtPd@PCN-224 nanoenzymes for signal amplification. Biosens Bioelectron 2023; 225:115098. [PMID: 36701949 DOI: 10.1016/j.bios.2023.115098] [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: 11/13/2022] [Revised: 01/06/2023] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
Abstract
In this work, PtPd nanoparticles functionalized porphyrin metal-organic framework nanoenzymes (PtPd@PCN-224 nanoenzymes) are exploited as signal amplification tags to fabricate a rapid and ultrasensitive sensitive CRISPR/Cas14a-based electrochemical biosensor for Burkholderia pseudomallei (B. pseudomallei) specific DNA sequences detection. The prepared PtPd@PCN-224 nanoenzymes not only catalyze the reduction peak current of H2O2 to obtain a strong electrochemical signal output, but also provide massive active sites for the assembly of nucleic acids by Zr-O-P bonds. Besides, the designed target-activated CRISPR/Cas14a is able to recognize the target DNA sequences and further trigger the trans-cleavage of ssDNA for signal amplification. Benefiting from the target-activated CRISPR/Cas14a and PtPd@PCN-224 nanoenzymes, the developed electrochemical biosensor for B. pseudomallei DNA detection exhibits high sensitivity with detection of limit down to 12.8 aM and excellent specificity for distinguishing non-targeted bacteria. Moreover, the CRISPR/Cas14a-based electrochemical detection platform can also apply for other pathogenic bacteria diagnostic by well-designing sgRNA for target sequence recognition, possessing high flexibility and versatility in clinical diagnosis.
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Affiliation(s)
- Cai Li
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Changjin Liu
- Department of Laboratory Medicine, The Fifth People's Hospital of Chongqing, Chongqing, 400062, China
| | - Rui Liu
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Yuexin Wang
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Anyang Li
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Shen Tian
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Wei Cheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Wenting Li
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China.
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
| | - Qianfeng Xia
- Department of Tropical Diseases of the Second Affiliated Hospital, Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China.
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5
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Fang B, Shen Y, Peng B, Bai H, Wang L, Zhang J, Hu W, Fu L, Zhang W, Li L, Huang W. Small‐Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism, and Applications. Angew Chem Int Ed Engl 2022; 61:e202207188. [DOI: 10.1002/anie.202207188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Bin Fang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- State Key Laboratory of Solidification Processing School of Materials Science and Engineering Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 China
| | - Yu Shen
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Limin Wang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Jiaxin Zhang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Wenbo Hu
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Li Fu
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- State Key Laboratory of Solidification Processing School of Materials Science and Engineering Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 China
| | - Wei Zhang
- Teaching and Evaluation Center of Air Force Medical University Xi'an 710032 China
| | - Lin Li
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- The Institute of Flexible Electronics (IFE, Future Technologies) Xiamen University Xiamen 361005, Fujian China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- The Institute of Flexible Electronics (IFE, Future Technologies) Xiamen University Xiamen 361005, Fujian China
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6
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Wongpalee SP, Thananchai H, Chewapreecha C, Roslund HB, Chomkatekaew C, Tananupak W, Boonklang P, Pakdeerat S, Seng R, Chantratita N, Takarn P, Khamnoi P. Highly specific and sensitive detection of Burkholderia pseudomallei genomic DNA by CRISPR-Cas12a. PLoS Negl Trop Dis 2022; 16:e0010659. [PMID: 36037185 PMCID: PMC9423629 DOI: 10.1371/journal.pntd.0010659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
Detection of Burkholderia pseudomallei, a causative bacterium for melioidosis, remains a challenging undertaking due to long assay time, laboratory requirements, and the lack of specificity and sensitivity of many current assays. In this study, we are presenting a novel method that circumvents those issues by utilizing CRISPR-Cas12a coupled with isothermal amplification to identify B. pseudomallei DNA from clinical isolates. Through in silico search for conserved CRISPR-Cas12a target sites, we engineered the CRISPR-Cas12a to contain a highly specific spacer to B. pseudomallei, named crBP34. The crBP34-based detection assay can detect as few as 40 copies of B. pseudomallei genomic DNA while discriminating against other tested common pathogens. When coupled with a lateral flow dipstick, the assay readout can be simply performed without the loss of sensitivity and does not require expensive equipment. This crBP34-based detection assay provides high sensitivity, specificity and simple detection method for B. pseudomallei DNA. Direct use of this assay on clinical samples may require further optimization as these samples are complexed with high level of human DNA. Melioidosis is a fatal infectious disease caused by a Gram-negative bacterium called Burkholderia pseudomallei. The bacteria can be found in many parts of the world, especially in the tropical and subtropical regions. Infection displays a variety of symptoms such as pneumonia, organ abscess and septicemia. The latter can lead to death within 24–48 hours if not properly diagnosed and treated. Rapid and accurate diagnosis, consequently, are essential for saving patients’ lives. Currently, culturing B. pseudomallei is a gold standard diagnostic method, but the assay turnaround time is 2–4 days, and the result could be of low sensitivity. Other detection methods such as real-time PCR and serological assays are limited by availability of equipment and by low specificity in endemic areas, respectively. For these reasons, in this study we developed a specific, sensitive and rapid detection assay for B. pseudomallei DNA, that is based on CRISPR-Cas12a system. The CRISPR-Cas12a is a protein-RNA complex that recognizes DNA. The RNA can be reprogramed to guide the detection of any DNA of interest, which in our case B. pseudomallei genomic DNA. Our data showed that this assay exhibited a 100% specificity to B. pseudomallei while discriminating against 10 other pathogens and human. The assay can detect B. pseudomallei DNA in less than one hour and does not require sophisticated equipment.
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Affiliation(s)
- Somsakul Pop Wongpalee
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| | - Hathairat Thananchai
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Henrik B. Roslund
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Warunya Tananupak
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phumrapee Boonklang
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sukritpong Pakdeerat
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Piyawan Takarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Phadungkiat Khamnoi
- Microbiology Unit, Diagnostic Laboratory, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai, Thailand
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7
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Fang B, Shen Y, Peng B, Bai H, Wang L, Zhang J, Hu W, Fu L, Zhang W, Li L, Huang W. Small Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism and Applications. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bin Fang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Yu Shen
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Bo Peng
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Hua Bai
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Limin Wang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Jiaxin Zhang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Wenbo Hu
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Li Fu
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Wei Zhang
- Air Force Medical University Teaching and Evaluation Center CHINA
| | - Lin Li
- Nanjing Tech University Institute of Advanced Materials 30 South Puzhu Road 210008 Nanjing CHINA
| | - Wei Huang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
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8
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Luo Z, Ye C, Xiao H, Yin J, Liang Y, Ruan Z, Luo D, Gao D, Tan Q, Li Y, Zhang Q, Liu W, Wu J. Optimization of loop-mediated isothermal amplification (LAMP) assay for robust visualization in SARS-CoV-2 and emerging variants diagnosis. Chem Eng Sci 2022; 251:117430. [PMID: 35043022 PMCID: PMC8757654 DOI: 10.1016/j.ces.2022.117430] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 11/24/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is widely used in detection of pathogenic microorganisms including SARS-CoV-2. However, the performance of LAMP assay needs further exploration in the emerging SARS-CoV-2 variants test. Here, we design serials of primers and select an optimal set for LAMP-based on SARS-CoV-2 N gene for a robust and visual assay in SARS-CoV-2 diagnosis. The limit of detectable template reaches 10 copies of N gene per 25 μL reaction at isothermal 58℃ within 40 min. Importantly, the primers for LAMP assay locate at 12 to 213 nt of N gene, a highly conservative region, which serves as a compatible test in emerging SARS-CoV-2 variants. Comparison to a commercial qPCR assay, this LAMP assay exerts the high viability in diagnosis of 41 clinical samples. Our study optimizes an advantageous LAMP assay for colorimetric detection of SARS-CoV-2 and emerging variants, which is hopeful to be a promising test in COVID-19 surveillance.
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Key Words
- COVID-19, coronavirus disease 2019
- CRISPR, clustered regularly interspaced short palindromic repeats
- Coronavirus disease 2019 (COVID-19) pandemic
- Ct, threshold cycle
- Emerging SARS-CoV-2 variants
- IVD, in-vitro diagnosis
- LAMP, Loop-mediated isothermal amplification
- Loop-mediated isothermal amplification (LAMP)
- NGS, next-generation sequencing
- POC, point-of-care
- RT-qPCR, real-time reverse transcriptase quantitative polymerase chain reaction
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis
- VOC, variants of concern
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Affiliation(s)
- Zhen Luo
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China.,Foshan Institute of Medical Microbiology, Foshan 528315, China
| | - Chunhong Ye
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
| | - Heng Xiao
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China.,Foshan Institute of Medical Microbiology, Foshan 528315, China
| | - Jialing Yin
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
| | - Yicong Liang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
| | - Zhihui Ruan
- Foshan Institute of Medical Microbiology, Foshan 528315, China
| | - Danju Luo
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Daolong Gao
- Guangdong Longfan Biological Science and Technology Company, Shunde District, Foshan 528315, China
| | - Qiuping Tan
- Guangdong Longfan Biological Science and Technology Company, Shunde District, Foshan 528315, China
| | - Yongkui Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China.,Foshan Institute of Medical Microbiology, Foshan 528315, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China.,Foshan Institute of Medical Microbiology, Foshan 528315, China
| | - Weiyong Liu
- Tongji Hospital of Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jianguo Wu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China.,Foshan Institute of Medical Microbiology, Foshan 528315, China.,Guangdong Longfan Biological Science and Technology Company, Shunde District, Foshan 528315, China
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9
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Li J, Zhong Q, Shang MY, Li M, Jiang YS, Zou JJ, Ma SS, Huang Q, Lu WP. Preliminary Evaluation of Rapid Visual Identification of Burkholderia pseudomallei Using a Newly Developed Lateral Flow Strip-Based Recombinase Polymerase Amplification (LF-RPA) System. Front Cell Infect Microbiol 2022; 11:804737. [PMID: 35118011 PMCID: PMC8804217 DOI: 10.3389/fcimb.2021.804737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/20/2021] [Indexed: 12/23/2022] Open
Abstract
Burkholderia pseudomallei is an important infectious disease pathogen that can cause melioidosis. Melioidosis is mainly prevalent in Thailand, northern Australia and southern China and has become a global public health problem. Early identification of B. pseudomallei is of great significance for the diagnosis and prognosis of melioidosis. In this study, a simple and visual device combined with lateral flow strip-based recombinase polymerase amplification (LF-RPA) was developed, and the utility of the LF-RPA assay for identifying B. pseudomallei was evaluated. In order to screen out the optimal primer probe, a total of 16 pairs of specific primers targeting the orf2 gene of B. pseudomallei type III secretion system (T3SS) cluster genes were designed for screening, and F1/R3 was selected as an optimal set of primers for the identification of B. pseudomallei, and parameters for LF-RPA were optimized. The LF-RPA can be amplified at 30-45°C and complete the entire reaction in 5-30 min. This reaction does not cross-amplify the DNA of other non-B. pseudomallei species. The limit of detection (LOD) of this assay for B. pseudomallei genomic DNA was as low as 30 femtograms (fg), which was comparable to the results of real-time PCR. Moreover, 21 clinical B. pseudomallei isolates identified by 16S rRNA gene sequencing were retrospectively confirmed by the newly developed LF-RPA system. Our results showed that the newly developed LF-RPA system has a simple and short time of operation and has good application prospect in the identification of B. pseudomallei.
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Affiliation(s)
- Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- Department of Laboratory Medicine, Ministry of Education (M.O.E.) Key Laboratory of Laboratory Medicine Diagnostics, Chongqing Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Mei-Yun Shang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Min Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yuan-Su Jiang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Jia-Jun Zou
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Shan-Shan Ma
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Wei-Ping Lu, ; Qing Huang,
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
- *Correspondence: Wei-Ping Lu, ; Qing Huang,
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Sun R, Zou H, Zhang Y, Zhang X, Chen L, Lv R, Sheng R, Du T, Li Y, Wang H, Qi Y. Vancomycin recognition and induced-aggregation of the Au nanoparticles through freeze-thaw for foodborne pathogen Staphylococcus aureus detection. Anal Chim Acta 2022; 1190:339253. [PMID: 34857141 DOI: 10.1016/j.aca.2021.339253] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 11/24/2022]
Abstract
Infectious diseases caused by foodborne pathogens have become a serious public health problem. It is urgent to develop simple, rapid, and visual methods for pathogen detection. Herein, gold nanoparticles (AuNPs), aptamer and vancomycin (Van) based dual-recognition molecules and magnetic enrichment were combined to realize visual detection of Staphylococcus aureus (S. aureus). Initially, S. aureus was bounded to aptamer coupled Fe3O4 with high affinity and selectivity, which can achieve the separation and enrichment of S. aureus in complex sample matrix. Subsequently, the second recognition molecule, Van, was conjugated to S. aureus -Apt - Fe3O4. Finally, the unbound Van supernatant was dropped in AuNPs solution that induced the aggregation of the AuNPs through freeze-thaw. Firstly, it was found that AuNPs were stable in the presence of Van after a freeze-thaw cycle. A facile visual colorimetric detection of S. aureus was constructed with the linear range from 101 to 104 CFU/mL and the limit of detection (LOD) of 0.2 CFU/mL. By altering the aptamer, this method can be extended to the other Gram-positive bacteria. The proposed method has great potential applications in monitoring food contamination and infectious diseases.
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Affiliation(s)
- Ruimeng Sun
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Hangjin Zou
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Yang Zhang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Xinming Zhang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Lixia Chen
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Ruijuan Lv
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Rongtian Sheng
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Ting Du
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Yuhan Li
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Han Wang
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China
| | - Yanfei Qi
- School of Public Health, Jilin University, Changchun, Jilin, 130021, PR China.
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