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Zhou C, Li W, Zhao Y, Gu K, Liao Z, Guo B, Huang Z, Yang M, Wei H, Ma P, Li C, Li H, Tang Y, Lei C, Wang H. Sensitive detection of viable salmonella bacteria based on tertiary cascade signal amplification via splintR ligase ligation-PCR amplification-CRISPR/Cas12a cleavage. Anal Chim Acta 2023; 1248:340885. [PMID: 36813454 DOI: 10.1016/j.aca.2023.340885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/04/2023] [Accepted: 01/22/2023] [Indexed: 01/24/2023]
Abstract
Several viable Salmonella bacteria are capable of causing severe human diseases and huge economic losses. In this regard, viable Salmonella bacteria detection techniques that can identify small numbers of microbial cells are highly valuable. Here, we present a detection method (referred to as SPC) based on the amplification of tertiary signals using splintR ligase ligation, PCR amplification and CRISPR/Cas12a cleavage. The detection limit of the SPC assay was 6 copies (HilA RNA) and 10 CFU (cell). Based on Intracellular HilA RNA detection, this assay can be used to distinguish between viable and dead Salmonella. In addition, it is able to detect multiple serotypes of Salmonella and has been successfully used to detect Salmonella in milk or isolated from farms. Overall, this assay is a promising test for viable pathogens detection and biosafety control.
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Affiliation(s)
- Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Wenjing Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ziwei Liao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Boyan Guo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Zheren Huang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Ming Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hongcheng Wei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Hao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Yizhi Tang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
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Fu X, Shi Y, Ma J, Zhang K, Wang G, Li G, Xiao L, Wang H. Advances of multiplex ligation-dependent probe amplification technology in molecular diagnostics. Biotechniques 2022; 73:205-213. [PMID: 36309987 DOI: 10.2144/btn-2022-0017] [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: 11/23/2022] Open
Abstract
Multiplex ligation-dependent probe amplification (MLPA) is a multiplex copy number analysis tool which is routinely used to detect large mutations in genetic diseases. With continuous modifications, MLPA has been extended for the detection of DNA methylation variation, single nucleotide polymorphisms, chromosome abnormalities and other forms of genomic variation. The combination with other techniques has even enlarged the application of MLPA in molecular diagnostics of various human diseases. In this review, the principle of MLPA-based techniques as well as their main and latest applications in clinical detection are described. It is believed that with improved automation, increased multiplexing, lower cost and the combination with other technologies, MLPA will play an increasingly important role in molecular diagnosis of human disease.
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Affiliation(s)
- Xiaoni Fu
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yinmin Shi
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jiying Ma
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Kaiqian Zhang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Guowei Wang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Gang Li
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Lei Xiao
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Huijuan Wang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
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3
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Zhang Y, Du XK, Liu WJ, Liu M, Zhang CY. Programmable Ligation-Transcription Circuit-Driven Cascade Amplification Machinery for Multiple Long Noncoding RNAs Detection in Lung Tissues. Anal Chem 2022; 94:10573-10578. [PMID: 35867839 DOI: 10.1021/acs.analchem.2c02685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measurement of long noncoding RNAs (lncRNAs) is essential to diagnosis and treatment of various diseases such as cancers. Herein, we develop a simple method to simultaneously detect multiple lncRNAs using programmable ligation-transcription circuit-driven cascade amplification and single-molecule counting. The presence of targets lncRNA HOTAIR and lncRNA MALAT1 activates the ligation-transcription circuits to produce two corresponding functional RNAs. The functional RNAs then cyclically initiate the digestion of signal probes by duplex-specific nuclease to liberate Cy5 and Cy3 molecules. After magnetic separation, the liberated Cy5 and Cy3 molecules are measured by single-molecule counting. In this assay, a single lncRNA can activate ligation-transcription circuit to generate abundant functional RNAs, endowing this assay with high sensitivity. Integration of single-molecule counting ensures the high sensitivity. This method shows extremely high sensitivity with a limit of detection (LOD) of 0.043 aM for HOX gene antisense intergenic RNA (lncRNA HOTAIR) and 0.126 aM for mammalian metastasis-related lung adenocarcinoma transcript 1 (lncRNA MALAT1). Importantly, this method enables simultaneous measurement of multiple endogenous lncRNAs at the single-cell level, and it may discriminate the expressions of various lncRNA in lung tumor tissues of nonsmall cell lung cancer (NSCLC) patients and their corresponding healthy adjacent tissues, offering a promising platform for clinical diagnosis and biomedical research.
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Affiliation(s)
- Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250200, China
| | - Xue-Ke Du
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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Sensitive fluorescence detection of SARS-CoV-2 RNA in clinical samples via one-pot isothermal ligation and transcription. Nat Biomed Eng 2020; 4:1168-1179. [PMID: 32948855 PMCID: PMC7499000 DOI: 10.1038/s41551-020-00617-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/27/2020] [Indexed: 01/12/2023]
Abstract
The control of viral outbreaks requires nucleic acid diagnostic tests that are sensitive, simple and fast. Here, we report a highly sensitive and specific one-pot assay for the fluorescence-based detection of RNA from pathogens. The assay, which can be performed within 30-50 min of incubation time and can reach a limit of detection of 0.1-attomolar RNA concentration, relies on a sustained isothermal reaction cascade producing an RNA aptamer that binds to a fluorogenic dye. The RNA aptamer is transcribed by the T7 RNA polymerase from the ligation product of a promoter DNA probe and a reporter DNA probe that hybridize with the target single-stranded RNA sequence via the SplintR ligase (a Chlorella virus DNA ligase). In 40 nasopharyngeal SARS-CoV-2 samples, the assay reached positive and negative predictive values of 95 and 100%, respectively. We also show that the assay can rapidly detect a range of viral and bacterial RNAs.
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Chung B, Park C, Cho SY, Shin J, Shin S, Yim SH, Lee DG, Chung YJ. Multiplex identification of sepsis-causing Gram-negative pathogens from the plasma of infected blood. Electrophoresis 2017; 39:645-652. [PMID: 29193166 DOI: 10.1002/elps.201700405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022]
Abstract
Early and accurate detection of bacterial pathogens in the blood is the most crucial step for sepsis management. Gram-negative bacteria are the most common organisms causing severe sepsis and responsible for high morbidity and mortality. We aimed to develop a method for rapid multiplex identification of clinically important Gram-negative pathogens and also validated whether our system can identify Gram-negative pathogens with the cell-free plasm DNA from infected blood. We designed five MLPA probe sets targeting the genes specific to major Gram-negative pathogens (uidA and lacY for E. coli, ompA for A. baumannii, phoE for K. pneumoniae, and ecfX for P. aeruginosa) and one set targeting the CTX-M group 1 to identify the ESBL producing Gram-negative pathogens. All six target-specific peaks were clearly separated without any non-specific peaks in a multiplex reaction condition. The minimum detection limit was 100 fg of pathogen DNA. When we tested 28 Gram-negative clinical isolates, all of them were successfully identified without any non-specific peaks. To evaluate the clinical applicability, we tested seven blood samples from febrile patients. Three blood culture positive cases showed E. coli specific peaks, while no peak was detected in the other four culture negative samples. This technology can be useful for detection of major sepsis-causing, drug-resistant Gram-negative pathogens and also the major ESBL producing Gram-negatives from the blood of sepsis patients in a clinical setting. This system can help early initiation of effective antimicrobial treatment against Gram-negative pathogens for sepsis patients, which is very crucial for better treatment outcomes.
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Affiliation(s)
- Boram Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea.,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Sun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea.,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Seon-Hee Yim
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea.,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary's Hospital, Seoul, Republic of Korea
| | - Yeun-Jung Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea.,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul, Republic of Korea
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Chung B, Park C, Cho SY, Shin S, Yim SH, Jung GY, Lee DG, Chung YJ. Multiplex identification of drug-resistant Gram-positive pathogens using stuffer-free MLPA system. Electrophoresis 2016; 37:3079-3083. [PMID: 27573990 DOI: 10.1002/elps.201600372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/09/2016] [Accepted: 08/22/2016] [Indexed: 11/09/2022]
Abstract
Early detection of pathogens from blood and identification of their drug resistance are essential for sepsis management. However, conventional culture-based methods require relatively longer time to identify drug-resistant pathogens, which delays therapeutic decisions. For precise multiplex detection of drug-resistant Gram-positive pathogens, we developed a method by using stuffer-free multiplex ligation-dependent probe amplification (MLPA) coupled with high-resolution CE single-strand conformation polymorphisms (CE-SSCP) system. We designed three probe sets for genes specific to Gram-positive species (Staphylococcus aureus: nuc, Enterococcus faecium: sodA, and Streptococcus pneumoniae: lytA) and two sets for genes associated with drug resistance (mecA and vanA) to discriminate major Gram-positive pathogens with the resistance. A total of 94 different strains (34 reference strains and 60 clinical isolates) were used to validate this method and strain-specific peaks were successfully observed for all the strains. To improve sensitivity of the method, a target-specific preamplification step was introduced and, consequently, the sensitivity increased from 10 pg to 100 fg. We also reduced a total assay time to 8 h by optimizing hybridization time without compromising test sensitivity. Taken together, our multiplex detection system can improve detection of drug-resistant Gram-positive pathogens from sepsis patients' blood.
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Affiliation(s)
- Boram Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sun Shin
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Seon-Hee Yim
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea Korea, Seoul, Korea
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Durney BC, Crihfield CL, Holland LA. Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014). Anal Bioanal Chem 2015; 407:6923-38. [PMID: 25935677 PMCID: PMC4551542 DOI: 10.1007/s00216-015-8703-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.
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Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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Chung B, Shin GW, Choi W, Joo J, Jeon S, Jung GY. Precise characterization method of antibody-conjugated magnetic nanoparticles for pathogen detection using stuffer-free multiplex ligation-dependent probe amplification. Electrophoresis 2014; 35:3283-9. [DOI: 10.1002/elps.201400180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 07/20/2014] [Accepted: 07/21/2014] [Indexed: 01/28/2023]
Affiliation(s)
- Boram Chung
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang Korea
| | - Gi Won Shin
- Institute of Environmental and Energy Technology; Pohang University of Science and Technology; Pohang Korea
| | - Woong Choi
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang Korea
| | - Jinmyoung Joo
- Department of Chemical Engineering; Pohang University of Science and Technology; Pohang Korea
| | - Sangmin Jeon
- Department of Chemical Engineering; Pohang University of Science and Technology; Pohang Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering; Pohang University of Science and Technology; Pohang Korea
- Department of Chemical Engineering; Pohang University of Science and Technology; Pohang Korea
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