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Marius M, Fernandez C. Non-Microbiological Mycobacterial Detection Techniques for Quality Control of Biological Products: A Comprehensive Review. Microorganisms 2024; 12:788. [PMID: 38674732 PMCID: PMC11052345 DOI: 10.3390/microorganisms12040788] [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: 03/14/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacteria can be one of the main contaminants of biological products, and their presence can have serious consequences on patients' health. For this reason, the European Pharmacopoeia mandates the specific testing of biological products for mycobacteria, a critical regulatory requirement aimed at ensuring the safety of these products before they are released to the market. The current pharmacopeial reference, i.e., microbial culture method, cannot ensure an exhaustive detection of mycobacteria due to their growth characteristics. Additionally, the method is time consuming and requires a continuous supply of culture media, posing logistical challenges. Thus, to overcome these issues, pharmaceutical industries need to consider alternative non-microbiological techniques to detect these fastidious, slow-growing contaminating agents. This review provides an overview of alternative methods, which could be applied within a quality control environment for biological products and underlines their advantages and limitations. Nucleic acid amplification techniques or direct measurement of mycobacteria stand out as the most suitable alternatives for mycobacterial testing in biological products.
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Affiliation(s)
- Marine Marius
- Sanofi, 1541 Ave. Marcel Mérieux, 69280 Marcy l’Etoile, France;
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2
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Czajka KM, Venkataraman K, Brabant-Kirwan D, Santi SA, Verschoor C, Appanna VD, Singh R, Saunders DP, Tharmalingam S. Molecular Mechanisms Associated with Antifungal Resistance in Pathogenic Candida Species. Cells 2023; 12:2655. [PMID: 37998390 PMCID: PMC10670235 DOI: 10.3390/cells12222655] [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: 10/17/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
Candidiasis is a highly pervasive infection posing major health risks, especially for immunocompromised populations. Pathogenic Candida species have evolved intrinsic and acquired resistance to a variety of antifungal medications. The primary goal of this literature review is to summarize the molecular mechanisms associated with antifungal resistance in Candida species. Resistance can be conferred via gain-of-function mutations in target pathway genes or their transcriptional regulators. Therefore, an overview of the known gene mutations is presented for the following antifungals: azoles (fluconazole, voriconazole, posaconazole and itraconazole), echinocandins (caspofungin, anidulafungin and micafungin), polyenes (amphotericin B and nystatin) and 5-fluorocytosine (5-FC). The following mutation hot spots were identified: (1) ergosterol biosynthesis pathway mutations (ERG11 and UPC2), resulting in azole resistance; (2) overexpression of the efflux pumps, promoting azole resistance (transcription factor genes: tac1 and mrr1; transporter genes: CDR1, CDR2, MDR1, PDR16 and SNQ2); (3) cell wall biosynthesis mutations (FKS1, FKS2 and PDR1), conferring resistance to echinocandins; (4) mutations of nucleic acid synthesis/repair genes (FCY1, FCY2 and FUR1), resulting in 5-FC resistance; and (5) biofilm production, promoting general antifungal resistance. This review also provides a summary of standardized inhibitory breakpoints obtained from international guidelines for prominent Candida species. Notably, N. glabrata, P. kudriavzevii and C. auris demonstrate fluconazole resistance.
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Affiliation(s)
- Karolina M. Czajka
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
| | - Krishnan Venkataraman
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
| | | | - Stacey A. Santi
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
| | - Chris Verschoor
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
| | - Vasu D. Appanna
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
| | - Ravi Singh
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
| | - Deborah P. Saunders
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
| | - Sujeenthar Tharmalingam
- Medical Sciences Division, NOSM University, 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada; (K.M.C.); (K.V.); (C.V.); (R.S.); (D.P.S.)
- School of Natural Sciences, Laurentian University, Sudbury, ON P3E 2C6, Canada;
- Health Sciences North Research Institute, Sudbury, ON P3E 2H2, Canada; (D.B.-K.); (S.A.S.)
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Lin Z, Sun B, Yang X, Jiang Y, Wu S, Lv B, Pan Y, Zhang Q, Wang X, Xiang G, Lou Y, Xiao X. Infectious Disease Diagnosis and Pathogen Identification Platform Based on Multiplex Recombinase Polymerase Amplification-Assisted CRISPR-Cas12a System. ACS Infect Dis 2023; 9:2306-2315. [PMID: 37811564 DOI: 10.1021/acsinfecdis.3c00381] [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: 10/10/2023]
Abstract
Controlling and mitigating infectious diseases caused by multiple pathogens or pathogens with several subtypes require multiplex nucleic acid detection platforms that can detect several target genes rapidly, specifically, sensitively, and simultaneously. Here, we develop a detection platform, termed Multiplex Assay of RPA and Collateral Effect of Cas12a-based System (MARPLES), based on multiplex nucleic acid amplification and Cas12a ssDNase activation to diagnose these diseases and identify their pathogens. We use the clinical specimens of hand, foot, and mouth disease (HFMD) and influenza A to evaluate the feasibility of MARPLES in diagnosing the disease and identifying the pathogen, respectively, and find that MARPLES can accurately diagnose the HFMD associated with enterovirus 71, coxsackievirus A16 (CVA16), CVA6, or CVA10 and identify the exact types of H1N1 and H3N2 in an hour, showing high sensitivity and specificity and 100% predictive agreement with qRT-PCR. Collectively, our findings demonstrate that MARPLES is a promising multiplex nucleic acid detection platform for disease diagnosis and pathogen identification.
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Affiliation(s)
- Ziqin Lin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Baochang Sun
- Department of Laboratory, Wenzhou Center for Disease Control and Prevention, Wenzhou 325035, China
| | - Xi Yang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yayun Jiang
- Department of Clinical Laboratory, People's Hospital of Deyang City, Deyang 618000, China
| | - Sihong Wu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Binbin Lv
- Department of Laboratory, Wenzhou Center for Disease Control and Prevention, Wenzhou 325035, China
| | - Yajing Pan
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Qingxun Zhang
- Beijing Milu Ecological Research Center, Beijing Academy of Science and Technology, Beijing 100076, China
| | - Xiaoqiong Wang
- Zhuji Institute of Biomedicine, Wenzhou Medical University, Zhuji, Shaoxing 311800, Zhejiang, China
| | - Guangxin Xiang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xingxing Xiao
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
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4
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Curtin K, Wang J, Fike BJ, Binkley B, Li P. A 3D printed microfluidic device for scalable multiplexed CRISPR-cas12a biosensing. Biomed Microdevices 2023; 25:34. [PMID: 37642743 DOI: 10.1007/s10544-023-00675-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] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Accurate, rapid, and multiplexed nucleic acid detection is critical for environmental and biomedical monitoring. In recent years, CRISPR-Cas12a has shown great potential in improving the performance of DNA biosensing. However, the nonspecific trans-cleavage activity of Cas12a complicates the multiplexing capability of Cas12a biosensing. We report a 3D-printed composable microfluidic plate (cPlate) device that utilizes miniaturized wells and microfluidic loading for a multiplexed CRISPR-Cas12a assay. The device easily combines loop-mediated isothermal amplification (LAMP) and CRISPR-Cas12a readout in a simple and high-throughput workflow with low reagent consumption. To ensure the maximum performance of the device, the concentration of Cas12a and detection probe was optimized, which yielded a four-fold sensitivity improvement. Our device demonstrates sensitive detection to the fg mL- 1 level for four waterborne pathogens including shigella, campylobacter, cholera, and legionella within 1 h, making it suitable for low-resource settings.
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Affiliation(s)
- Kathrine Curtin
- Department of Mechanical and Aerospace Engineering, West Virginia University, Morgantown, WV, USA
| | - Jing Wang
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Bethany J Fike
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Brandi Binkley
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA.
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Filippova AA, Presnova GV, Grigorenko VG, Ulyashova MM, Rubtsova MY. A Method for Processing Digital Images of Colorimetric Biochips for Quantitative Determination of Bacterial Antibiotic Resistance Genes. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822090046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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6
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Tellurium-Modified Nucleosides, Nucleotides, and Nucleic Acids with Potential Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238379. [PMID: 36500495 PMCID: PMC9737395 DOI: 10.3390/molecules27238379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main synthetic approaches for the preparation of 5-PhTe, 2'-MeTe, and 2'-PhTe modifications. Those modifications are compatible with solid-phase synthesis and stable during Te-oligonucleotide purification. Moreover, the ideal electronic and atomic properties of tellurium for generating clear isomorphous signals give Te-modified DNA and RNA great potential applications in 3D crystal structure determination through X-ray diffraction. STM study also shows that Te-modified DNA has strong topographic and current peaks, which immediately suggests potential applications in nucleic acid direct imaging, nanomaterials, molecular electronics, and diagnostics. Theoretical studies indicate the potential application of Te-modified nucleosides in cancer therapy.
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7
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Gao H, Shang Z, Chan SY, Ma D. Recent advances in the use of the CRISPR-Cas system for the detection of infectious pathogens. J Zhejiang Univ Sci B 2022; 23:881-898. [PMID: 36379609 PMCID: PMC9676091 DOI: 10.1631/jzus.b2200068] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Infectious diseases cause great economic loss and individual and even social anguish. Existing detection methods lack sensitivity and specificity, have a poor turnaround time, and are dependent on expensive equipment. In recent years, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) system has been widely used in the detection of pathogens that cause infectious diseases owing to its high specificity, sensitivity, and speed, and good accessibility. In this review, we discuss the discovery and development of the CRISPR-Cas system, summarize related analysis and interpretation methods, and discuss the existing applications of CRISPR-based detection of infectious pathogens using Cas proteins. We conclude the challenges and prospects of the CRISPR-Cas system in the detection of pathogens.
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Affiliation(s)
- Hongdan Gao
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518026, China
| | - Zifang Shang
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518026, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Siew Yin Chan
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China
| | - Dongli Ma
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518026, China.
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8
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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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9
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CRISPR-Cas-mediated diagnostics. Trends Biotechnol 2022; 40:1326-1345. [PMID: 35595574 DOI: 10.1016/j.tibtech.2022.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 01/21/2023]
Abstract
An ideal molecular diagnostic method should be sensitive, specific, low cost, rapid, portable, and easy to operate. Traditional nucleic acid detection methods based mainly on PCR technology have not only high sensitivity and specificity, but also some limitations, such as the need for expensive equipment and skilled technicians, being both time and labor intensive, and difficult to implement in some regions. However, with the continuous development of CRISPR-Cas technology and its application in molecular diagnosis, new approaches have been used for the construction of molecular diagnostic systems. In this review, we discuss recent advances in CRISPR-based molecular diagnostic technologies and highlight the revolution they bring to the field of molecular diagnostics.
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10
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Rajan A, Shrivastava S, Janhawi, Kumar A, Singh AK, Arora PK. CRISPR-Cas system: from diagnostic tool to potential antiviral treatment. Appl Microbiol Biotechnol 2022; 106:5863-5877. [PMID: 36008567 PMCID: PMC9411046 DOI: 10.1007/s00253-022-12135-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
This mini review focuses on the diagnosis and treatment of virus diseases using Crisper-Cas technology. The present paper describes various strategies involved in diagnosing diseases using Crispr-Cas-based assays. Additionally, CRISPR-Cas systems offer great potential as new therapeutic tools for treating viral infections including HIV, Influenza, and SARS-CoV-2. There are several major challenges to be overcome before this technology can be applied routinely in clinical settings, such as finding a suitable delivery tool, toxicity, and immunogenicity, as well as off-target effects. This review also discusses ways to deal with the challenges associated with Crisper-Cas technology. KEY POINTS: • Crisper technology is being applied to diagnose infectious and non-infectious diseases. • A new generation of CRISPR-Cas-based assays has been developed which detect pathogens within minutes, providing rapid diagnosis of diseases. • Crispr-Cas tools can be used to combat viral infections, specifically HIV, influenza, and SARS-CoV-2.
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Affiliation(s)
- Aishwarya Rajan
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Stuti Shrivastava
- Electronics and Communication, Jaypee Institute of Information Technology, Noida, India
| | - Janhawi
- Department of Zoology, Kalindi College, University of Delhi, Delhi, India
| | - Akhilesh Kumar
- Department of Botany, Banaras Hindu University, Varanasi, India.
| | - Alok Kumar Singh
- Department of Biochemistry, Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, Delhi, India.
| | - Pankaj Kumar Arora
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India.
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Mao X, Zhao Y, Jiang J, Du Q, Tu B, Li J, Wang F. Sensitive and high-accuracy detection of Salmonella based on CRISPR/Cas12a combined with recombinase polymerase amplification. Lett Appl Microbiol 2022; 75:899-907. [PMID: 35694840 DOI: 10.1111/lam.13765] [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: 02/18/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022]
Abstract
Salmonella is a crucial food-borne pathogen causing food poisoning, leading to severe public health events. Here, we developed a technique by integrating recombinase polymerase amplification with CRISPR-LbCas12a and employing two targets with engineered crRNA for detection of Salmonella (RPA-LbCas12a-TTECDS). Our findings revealed that this novel method rapidly detects trace Salmonella in food through fluorescence intensity and provides a template for other food-borne pathogen detection methods. Further, crRNA was optimized to increase detection sensitivity. Double targets were used to enhance the detection accuracy, reaching the level of qPCR, which was superior to fluorescent RPA. The RPA-LbCas12a-TTECDS system specifically detected Salmonella levels as low as 50 CFU per ml at 37°C in 1 h. In summary, a simple, rapid, sensitive and high accuracy detection technique based on CRISPR-Cas12a was created for Salmonella detection without complicated equipment.
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Affiliation(s)
- X Mao
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, China
| | - Y Zhao
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, China
| | - J Jiang
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, China
| | - Q Du
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, China
| | - B Tu
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, China
| | - J Li
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, China
| | - F Wang
- Pathogen Inspection Center, Changzhou Center for Disease Prevention and Control, Changzhou, China
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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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13
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Multiplex Digital Quantification of β-Lactamase Genes in Antibiotic-Resistant Bacteria by Counting Gold Nanoparticle Labels on Silicon Microchips. BIOSENSORS 2022; 12:bios12040226. [PMID: 35448287 PMCID: PMC9024738 DOI: 10.3390/bios12040226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022]
Abstract
Digital quantification based on counting of individual molecules is a promising approach for different biomedical applications due to its enhanced sensitivity. Here, we present a method for the digital detection of nucleic acids (DNA and RNA) on silicon microchips based on the counting of gold nanoparticles (GNPs) in DNA duplexes by scanning electron microscopy (SEM). Biotin-labeled DNA is hybridized with capture oligonucleotide probes immobilized on the microchips. Then biotin is revealed by a streptavidin–GNP conjugate followed by the detection of GNPs. Sharp images of each nanoparticle allow the visualization of hybridization results on a single-molecule level. The technique was shown to provide highly sensitive quantification of both short oligonucleotide and long double-strand DNA sequences up to 800 bp. The lowest limit of detection of 0.04 pM was determined for short 19-mer oligonucleotide. The method’s applicability was demonstrated for the multiplex quantification of several β-lactamase genes responsible for the development of bacterial resistance against β-lactam antibiotics. Determination of nucleic acids is effective for both specific DNA in lysates and mRNA in transcripts. The method is also characterized by high selectivity for single-nucleotide polymorphism discrimination. The proposed principle of digital quantification is a perspective for studying the mechanisms of bacterial antibiotic resistance and bacterial response to drugs.
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You H, Gordon CA, MacGregor SR, Cai P, McManus DP. Potential of the CRISPR-Cas system for improved parasite diagnosis: CRISPR-Cas mediated diagnosis in parasitic infections: CRISPR-Cas mediated diagnosis in parasitic infections. Bioessays 2022; 44:e2100286. [PMID: 35142378 DOI: 10.1002/bies.202100286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas technology accelerates development of fast, accurate, and portable diagnostic tools, typified by recent applications in COVID-19 diagnosis. Parasitic helminths cause devastating diseases afflicting 1.5 billion people globally, representing a significant public health and economic burden, especially in developing countries. Currently available diagnostic tests for worm infection are neither sufficiently sensitive nor field-friendly for use in low-endemic or resource-poor settings, leading to underestimation of true prevalence rates. Mass drug administration programs are unsustainable long-term, and diagnostic tools - required to be rapid, specific, sensitive, cost-effective, and user-friendly without specialized equipment and expertise - are urgently needed for rapid mapping of helminthic diseases and monitoring control programs. We describe the key features of the CRISPR-Cas12/13 system and emphasise its potential for the development of effective tools for the diagnosis of parasitic and other neglected tropical diseases (NTDs), a key recommendation of the NTDs 2021-2030 roadmap released by the World Health Organization.
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Affiliation(s)
- Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Catherine A Gordon
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Skye R MacGregor
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Pengfei Cai
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Donald P McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
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15
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Meng Q, Yang H, Zhang G, Sun W, Ma P, Liu X, Dang L, Li G, Huang X, Wang X, Liu J, Leng Q. CRISPR/Cas12a-assisted rapid identification of key beer spoilage bacteria. INNOV FOOD SCI EMERG 2021. [DOI: 10.1016/j.ifset.2021.102854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Fu J, Li J, Chen J, Li Y, Liu J, Su X, Shi S. Ultra-specific nucleic acid testing by target-activated nucleases. Crit Rev Biotechnol 2021; 42:1061-1078. [PMID: 34706599 DOI: 10.1080/07388551.2021.1983757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.
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Affiliation(s)
- Jinyu Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yabei Li
- Department of Neurosurgery, People's Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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Ge X, Meng T, Tan X, Wei Y, Tao Z, Yang Z, Song F, Wang P, Wan Y. Cas14a1-mediated nucleic acid detectifon platform for pathogens. Biosens Bioelectron 2021; 189:113350. [PMID: 34049081 DOI: 10.1016/j.bios.2021.113350] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 12/26/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated nuclease (Cas) based biosensing system provides a novel genomic diagnostic tool for pathogenic detection. However, most of the discovered Cas effectors have poor single strand DNA (ssDNA) target recognition capability with the constraint of protospacer adjacent motif (PAM) sites, which are not suitable for universal pathogenic diagnosis. Herein, we developed a highly sensitive and specific fluorescence tool for bacterial detection by utilizing the unique collateral cleavage activity of a Cas14a1-mediated nucleic acid detection platform (CMP). We combine CMP with molecular amplification to build a CRISPR-Cas based bioanalysis technique, offering fast nucleic acid detection with high sensitivity and specificity. This technique can identify different species of pathogens in milk samples with excellent accuracy. The CMP technique is a promising platform for pathogenic genomic diagnostic in biomedicine and food safety field.
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Affiliation(s)
- Xiaolin Ge
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Tian Meng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Xiao Tan
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yangdao Wei
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Zhenzhen Tao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Zhiqing Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Fengge Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China
| | - Peng Wang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou, 570228, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, PR China; CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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18
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Higgins O, Smith TJ. 3' Tth Endonuclease Cleavage Polymerase Chain Reaction (3TEC-PCR) Technology for Single-Base-Specific Multiplex Pathogen Detection using a Two-Oligonucleotide System. Int J Mol Sci 2021; 22:6061. [PMID: 34199760 PMCID: PMC8199996 DOI: 10.3390/ijms22116061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
Polymerase chain reaction (PCR) is the standard in nucleic acid amplification technology for infectious disease pathogen detection and has been the primary diagnostic tool employed during the global COVID-19 pandemic. Various PCR technology adaptations, typically using two-oligonucleotide dye-binding methods or three-oligonucleotide hydrolysis probe systems, enable real-time multiplex target detection or single-base specificity for the identification of single-nucleotide polymorphisms (SNPs). A small number of two-oligonucleotide PCR systems facilitating both multiplex detection and SNP identification have been reported; however, these methods often have limitations in terms of target specificity, production of variable or false-positive results, and the requirement for extensive optimisation or post-amplification analysis. This study introduces 3' Tth endonuclease cleavage PCR (3TEC-PCR), a two-oligonucleotide PCR system incorporating a modified primer/probe and a thermostable cleavage enzyme, Tth endonuclease IV, for real-time multiplex detection and SNP identification. Complete analytical specificity, low limits of detection, single-base specificity, and simultaneous multiple target detection have been demonstrated in this study using 3TEC-PCR to identify bacterial meningitis associated pathogens. This is the first report of a two-oligonucleotide, real-time multiplex PCR technology with single-base specificity using Tth endonuclease IV.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland;
- Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Terry J. Smith
- Molecular Diagnostics Research Group, School of Natural Sciences, National University of Ireland, Galway, Ireland;
- Centre for One Health, Ryan Institute, National University of Ireland, Galway, Ireland
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Schulze H, Arnott A, Libori A, Obaje EA, Bachmann TT. Temperature-Enhanced mcr-1 Colistin Resistance Gene Detection with Electrochemical Impedance Spectroscopy Biosensors. Anal Chem 2021; 93:6025-6033. [PMID: 33819015 DOI: 10.1021/acs.analchem.0c00666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibiotic resistance is now one of the biggest threats humankind is facing, as highlighted in a declaration by the General Assembly of the United Nations in 2016. In particular, the growing resistance rates of Gram-negative bacteria cause increasing concerns. The occurrence of the easily transferable, plasmid-encoded mcr-1 colistin resistance gene further worsened the situation, significantly enhancing the risk of the occurrence of pan-resistant bacteria. There is therefore a strong demand for new rapid molecular diagnostic tests for the detection of mcr-1 gene-associated colistin resistance. Electrochemical impedance spectroscopy (EIS) is a well-suited method for rapid antimicrobial resistance detection as it enables rapid, label-free target detection in a cost-efficient manner. Here, we describe the development of an EIS-based mcr-1 gene detection test, including the design of mcr-1-specific peptide nucleic acid probes and assay specificity optimization through temperature-controlled real-time kinetic EIS measurements. A new flow cell measurement setup enabled for the first time detailed real-time, kinetic temperature-controlled hybridization and dehybridization studies of EIS-based nucleic acid biosensors. The temperature-controlled EIS setup allowed single-nucleotide polymorphism discrimination. Target hybridization at 60 °C enhanced the perfect match/mismatch (PM/MM) discrimination ratio from 2.1 at room temperature to 3.4. A hybridization and washing temperature of 55 °C further increased the PM/MM discrimination ratio to 5.7 by diminishing the mismatch signal during the washing step while keeping the perfect match signal. This newly developed mcr-1 gene detection test enabled the direct, specific label, and amplification-free detection of mcr-1 gene harboring plasmids from Escherichia coli.
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Affiliation(s)
- Holger Schulze
- Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, U.K
| | - Andrew Arnott
- Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, U.K
| | - Adriana Libori
- Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, U.K
| | - Eleojo A Obaje
- Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, U.K
| | - Till T Bachmann
- Infection Medicine, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, U.K
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20
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Luo F, Lu Y, Geng X, Li Z, Dai G, Chu Z, Zhang J, Zhang F, He P, Wang Q. Study on Defective T Junction-Mediated Strand Displacement Amplification and Its Application in Microchip Electrophoretic Detection of Longer Bacterial 16S rDNA. Anal Chem 2021; 93:3551-3558. [PMID: 33570925 DOI: 10.1021/acs.analchem.0c04991] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Current strand displacement amplification (SDA)-based nucleic acid sensing methods generally rely on a ssDNA template that involves complementary bases to the endonuclease recognition sequence, which has the limitation of detecting only short nucleic acids. Herein, a new SDA method in which the defective T junction structure is first used to support SDA (dT-SDA) was proposed and applied in longer DNA detection. In dT-SDA, an auxiliary probe and a primer were designed to specifically identify the target gene, following the formation of a stable defective T junction structure through proximity hybridization, and the formation of defective T junctions could further trigger cascade SDA cycling to produce numerous ssDNA products. The quantity of these ssDNA products was detected through microchip electrophoresis (MCE) and could be transformed to the concentration of the target gene. Moreover, the applicability of this developed strategy in detecting long genomic DNA was verified by detecting bacterial 16S rDNA. This proposed dT-SDA strategy consumes less time and has satisfactory sensitivity, which has great potential for effective bacterial screening and infection diagnosis.
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Affiliation(s)
- Feifei Luo
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Yuqi Lu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Xing Geng
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Zhi Li
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Ge Dai
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Zhaohui Chu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Jingwen Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Pingang He
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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21
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Satish L, Lavanya G, Kasthuri T, Kalaivaani A, Shamili S, Muthuramalingam P, Gowrishankar S, Pandian SK, Singh V, Sitrit Y, Kushmaro A. CRISPR based development of RNA editing and the diagnostic platform. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 179:117-159. [PMID: 33785175 DOI: 10.1016/bs.pmbts.2020.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Clustered Regularly Interspersed Short Palindromic Repeat-CRISPR-Associated (CRISPR-Cas) system has improved the ability to edit and control gene expression as desired. Genome editing approaches are currently leading the biomedical research with improved focus on direct nuclease dependent editing. So far, the research was predominantly intended on genome editing over the DNA level, recent adapted techniques are initiating to secure momentum through their proficiency to provoke modifications in RNA sequence. Integration of this system besides to lateral flow method allows reliable, quick, sensitive, precise and inexpensive diagnostic. These interesting methods illustrate only a small proportion of what is technically possible for this novel technology, but several technological obstacles need to be overcome prior to the CRISPR-Cas genome editing system can meet its full ability. This chapter covers the particulars on recent advances in CRISPR-Cas9 genome editing technology including diagnosis and technical advancements, followed by molecular mechanism of CRISPR-based RNA editing and diagnostic tools and types, and CRISPR-Cas-based biosensors.
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Affiliation(s)
- Lakkakula Satish
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel; The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Bergman Campus, Beer Sheva, Israel
| | - Gunamalai Lavanya
- Department of Postharvest and Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Thirupathi Kasthuri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Aruchamy Kalaivaani
- Department of Postharvest and Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Sasanala Shamili
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Bergman Campus, Beer Sheva, Israel
| | | | | | | | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Yaron Sitrit
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Bergman Campus, Beer Sheva, Israel
| | - Ariel Kushmaro
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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22
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Paper-Based Nucleic Acid Detection for Point-of-Care Diagnostics. Bioanalysis 2021. [DOI: 10.1007/978-981-15-8723-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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23
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Wang X, Shang X, Huang X. Next-generation pathogen diagnosis with CRISPR/Cas-based detection methods. Emerg Microbes Infect 2020; 9:1682-1691. [PMID: 32643563 PMCID: PMC7473117 DOI: 10.1080/22221751.2020.1793689] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023]
Abstract
Ideal methods for detecting pathogens should be sensitive, specific, rapid, cost-effective and instrument-free. Conventional nucleic acid pathogen detection strategies, mostly PCR-based techniques, have various limitations, such as expensive equipment, reagents and skilled performance. Recently, CRISPR/Cas-based methods have burst onto the scene, with the potential to power the pathogen detection field. Here we introduce these unique methods and discuss its hurdles and promises.
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Affiliation(s)
- Xinjie Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Xiaoyun Shang
- Suzhou Maximum Bio-tech Co., Ltd., Suzhou, People’s Republic of China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
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Sidhu JPS, Gupta VVSR, Stange C, Ho J, Harris N, Barry K, Gonzalez D, Van Nostrand JD, Zhou J, Page D, Tiehm A, Toze S. Prevalence of antibiotic resistance and virulence genes in the biofilms from an aquifer recharged with stormwater. WATER RESEARCH 2020; 185:116269. [PMID: 32798893 DOI: 10.1016/j.watres.2020.116269] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
An improved understanding of the diversity and composition of microbial communities carrying antibiotic resistance genes (ARGs) and virulence genes (VGs) in aquifers recharged with stormwater is essential to comprehend potential human health risks from water reuse. A high-throughput functional gene array was used to study the prevalence of ARGs and VGs in aquifer biofilms (n = 27) taken from three boreholes over three months. Bacterial genera annotated as opportunistic pathogens such as Aeromonas, Burkholderia, Pseudomonas, Shewanella, and Vibrio were ubiquitous and abundant in all biofilms. Bacteria from clinically relevant genera, Campylobacter, Enterobacter, Klebsiella, Mycobacterium, Mycoplasma, and Salmonella were detected in biofilms. The mean travel time of stormwater from the injection well to P1 and P3 boreholes was 260 and 360 days respectively. The presence of ARGs and VGs in the biofilms from these boreholes suggest a high spatial movement of ARGs and VGs in the aquifer. The ARGs with the highest abundance were small multidrug resistance efflux pumps (SMR) and multidrug efflux (Mex) followed by β-lactamase C genes. β- lactamase C encoding genes were primarily detected in Enterobacteriaceae, Pseudomonadaceae, Bacillaceae, and Rhodobacteraceae families. The VGs encoding siderophores, including aerobactin (iro and iuc genes), followed by pilin, hemolysin, and type III secretion were ubiquitous. Canonical correspondence analysis suggested that Total Organic Carbon (TOC), Dissolved Organic Carbon (DOC), turbidity, and Fe concentration has a significant impact on the microbial community structure of bacteria carrying ARGs and VGs. Post abstraction treatment of groundwater may be prudent to improve water security and reduce potential health risks.
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Affiliation(s)
- J P S Sidhu
- CSIRO Oceans and Atmosphere, Ecoscience Precinct, 41 Boggo Road, Brisbane 4102, Australia.
| | - V V S R Gupta
- CSIRO Agriculture and Food, Locked Bag No. 2, Glen Osmond, SA 5064, Australia
| | - C Stange
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Street 84, D-76139 Karlsruhe, Germany
| | - J Ho
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Street 84, D-76139 Karlsruhe, Germany
| | - N Harris
- CSIRO Agriculture and Food, Locked Bag No. 2, Glen Osmond, SA 5064, Australia
| | - K Barry
- CSIRO Land and Water Private Bag 2, Glen Osmond, SA 5064, Australia
| | - D Gonzalez
- CSIRO Land and Water Private Bag 2, Glen Osmond, SA 5064, Australia
| | - J D Van Nostrand
- Institute of Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
| | - J Zhou
- Institute of Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
| | - D Page
- CSIRO Land and Water Private Bag 2, Glen Osmond, SA 5064, Australia
| | - A Tiehm
- DVGW-Technologiezentrum Wasser (TZW), Karlsruher Street 84, D-76139 Karlsruhe, Germany
| | - S Toze
- CSIRO Land and Water, Ecoscience Precinct, 41 Boggo Road, Brisbane 4102, Australia
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25
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van Dongen JE, Berendsen JTW, Steenbergen RDM, Wolthuis RMF, Eijkel JCT, Segerink LI. Point-of-care CRISPR/Cas nucleic acid detection: Recent advances, challenges and opportunities. Biosens Bioelectron 2020; 166:112445. [PMID: 32758911 PMCID: PMC7382963 DOI: 10.1016/j.bios.2020.112445] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022]
Abstract
With the trend of moving molecular tests from clinical laboratories to on-site testing, there is a need for nucleic acid based diagnostic tools combining the sensitivity, specificity and flexibility of established diagnostics with the ease, cost effectiveness and speed of isothermal amplification and detection methods. A promising new nucleic acid detection method is Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated nuclease (Cas)-based sensing. In this method Cas effector proteins are used as highly specific sequence recognition elements that can be combined with many different read-out methods for on-site point-of-care testing. This review covers the technical aspects of integrating CRISPR/Cas technology in miniaturized sensors for analysis on-site. We start with a short introduction to CRISPR/Cas systems and the different effector proteins and continue with reviewing the recent developments of integrating CRISPR sensing in miniaturized sensors for point-of-care applications. Finally, we discuss the challenges of point-of-care CRISPR sensing and describe future research perspectives.
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Affiliation(s)
- Jeanne E van Dongen
- BIOS Lab on a Chip group, Technical Medical Centre, MESA+ Institute for Nanotechnology, University of Twente, P.O. box 217, 7500, AE, Enschede, the Netherlands.
| | - Johanna T W Berendsen
- BIOS Lab on a Chip group, Technical Medical Centre, MESA+ Institute for Nanotechnology, University of Twente, P.O. box 217, 7500, AE, Enschede, the Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Clinical Genetics, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Jan C T Eijkel
- BIOS Lab on a Chip group, Technical Medical Centre, MESA+ Institute for Nanotechnology, University of Twente, P.O. box 217, 7500, AE, Enschede, the Netherlands
| | - Loes I Segerink
- BIOS Lab on a Chip group, Technical Medical Centre, MESA+ Institute for Nanotechnology, University of Twente, P.O. box 217, 7500, AE, Enschede, the Netherlands
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Ma P, Meng Q, Sun B, Zhao B, Dang L, Zhong M, Liu S, Xu H, Mei H, Liu J, Chi T, Yang G, Liu M, Huang X, Wang X. MeCas12a, a Highly Sensitive and Specific System for COVID-19 Detection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001300. [PMID: 33042732 PMCID: PMC7536916 DOI: 10.1002/advs.202001300] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/30/2020] [Indexed: 05/04/2023]
Abstract
Cas12a-based systems, which detect specific nucleic acids via collateral cleavage of reporter DNA, display huge potentials for rapid diagnosis of infectious diseases. Here, the Manganese-enhanced Cas12a (MeCas12a) system is described, where manganese is used to increase the detection sensitivity up to 13-fold, enabling the detection of target RNAs as low as five copies. MeCas12a is also highly specific, and is able to distinguish between single nucleotide polymorphisms (SNPs) differing by a single nucleotide. MeCas12a can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples and distinguish between SARS-CoV-2 and Middle East respiratory syndrome coronavirus (MERS-CoV) RNA in simulated samples, thus offering an attractive alternative to other methods for the diagnosis of infectious diseases including COVID-19 and MERS.
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Affiliation(s)
- Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Qingzhou Meng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University78 Hengzhigang RoadGuangzhou510095China
| | - Baoqing Sun
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated HospitalGuangzhou Medical UniversityGuangzhou510120China
| | - Bing Zhao
- Microbiological Testing LaboratoryShanghai Pudong New Area Center for Disease Control and PreventionShanghai200136China
| | - Lu Dang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University78 Hengzhigang RoadGuangzhou510095China
| | - Mingtian Zhong
- Institute for Brain Research and RehabilitationGuangdong Key Laboratory of Mental Health and Cognitive ScienceCenter for Studies of Psychological ApplicationSouth China Normal UniversityGuangzhou510631China
| | - Siyuan Liu
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Hong Mei
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Tian Chi
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Ming Liu
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated HospitalGuangzhou Medical UniversityGuangzhou510120China
| | - Xingxu Huang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xinjie Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
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Zhang D, Yan Y, Que H, Yang T, Cheng X, Ding S, Zhang X, Cheng W. CRISPR/Cas12a-Mediated Interfacial Cleaving of Hairpin DNA Reporter for Electrochemical Nucleic Acid Sensing. ACS Sens 2020; 5:557-562. [PMID: 32013399 DOI: 10.1021/acssensors.9b02461] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A rapid and sensitive isothermal method is crucial for point-of-care (POC) nucleic acid testing. Recently, RNA-guided CRISPR/Cas12a proteins were discovered to exhibit target-triggered nonspecific single-stranded deoxyribonuclease (ssDNase) activity. Herein, the ssDNase cleavage capacity of the CRISPR/Cas12a system for interfacial hairpin DNA (hpDNA) and linear DNA was investigated in detailed. A novel electrochemical DNA biosensor was then developed via target-induced Cas12a cleaving interfacial hpDNA. In this strategy, the RNA-guided target DNA binding activates the robust Cas12a ssDNase activity. The immobilized hpDNA electrochemical reporters with a low surface coverage and incompact morphological structure present accessible substrates for highly efficient Cas12a cleavage, leading to a highly sensitive electrochemical DNA biosensor. Under the optimal conditions, as low as 30 pM target DNA was detected in about 60 min with 3.5 orders of magnitude dynamic range from 50 pM to 100 nM. Furthermore, the practical application ability of the established sensing method for detecting the target in complex matrices was also demonstrated. The proposed strategy enables rapid and sensitive DNA determination, providing a potential tool for POC molecular diagnostics.
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Affiliation(s)
- Decai Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Haiying Que
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaoxue Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of 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
| | - Xiuming Zhang
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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CRISPR/Cas Systems towards Next-Generation Biosensing. Trends Biotechnol 2019; 37:730-743. [PMID: 30654914 DOI: 10.1016/j.tibtech.2018.12.005] [Citation(s) in RCA: 482] [Impact Index Per Article: 96.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023]
Abstract
Beyond its remarkable genome editing ability, the CRISPR/Cas9 effector has also been utilized in biosensing applications. The recent discovery of the collateral RNA cleavage activity of the Cas13a effector has sparked even greater interest in developing novel biosensing technologies for nucleic acid detection and promised significant advances in CRISPR diagnostics. Now, along with the discovery of Cas12 collateral cleavage activities on single-stranded DNA (ssDNA), several CRISPR/Cas systems have been established for detecting various targets, including bacteria, viruses, cancer mutations, and others. Based on key Cas effectors, we provide a detailed classification of CRISPR/Cas biosensing systems and propose their future utility. As the field continues to mature, CRISPR/Cas systems have the potential to become promising candidates for next-generation diagnostic biosensing platforms.
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Teratanatorn P, Hoskins R, Swift T, Douglas CWI, Shepherd J, Rimmer S. Binding of Bacteria to Poly(N-isopropylacrylamide) Modified with Vancomycin: Comparison of Behavior of Linear and Highly Branched Polymers. Biomacromolecules 2017; 18:2887-2899. [PMID: 28731679 DOI: 10.1021/acs.biomac.7b00800] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The behavior of a linear copolymer of N-isopropylacrylamide with pendant vancomycin functionality was compared to an analogous highly branched copolymer with vancomycin functionality at the chain ends. Highly branched poly(N-isopropylacrylamide) modified with vancomycin (HB-PNIPAM-van) was synthesized by functionalization of the HB-PNIPAM, prepared using reversible addition-fragmentation chain transfer polymerization. Linear PNIPAM with pendant vancomycin functionality (L-PNIPAM-van) was synthesized by functionalization of poly(N-isopropylacrylamide-co-vinyl benzoic acid). HB-PNIPAM-van aggregated S. aureus effectively, whereas the L-PNIPAM-van polymer did not. It was found that when the HB-PNIPAM-van was incubated with S. aureus the resultant phase transition provided an increase in the intensity of fluorescence of a solvatochromic dye, nile red, added to the system. In contrast, a significantly lower increase in fluorescence intensity was obtained when L-PNIPAM-van was incubated with S. aureus. These data showed that the degree of desolvation of HB-PNIPAM-van was much greater than the desolvation of the linear version. Using microcalorimetry, it was shown that there were no significant differences in the affinities of the polymer ligands for d-Ala-d-Ala and therefore differences in the interactions with bacteria were associated with changes in the probability of access of the polymer bound ligands to the d-Ala-d-Ala dipeptide. The data support the hypothesis that generation of polymer systems that respond to cellular targets, for applications such as cell targeting, detection of pathogens etc., requires the use of branched polymers with ligands situated at the chain ends.
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Affiliation(s)
- Pavintorn Teratanatorn
- Dental School, University of Sheffield , 19 Claremont Crescent, Sheffield, South Yorkshire, U.K. , S10 2TA
| | - Richard Hoskins
- School of Chemistry and Biosciences, University of Bradford , Bradford, West Yorkshire, U.K. , BD1 1DP
| | - Thomas Swift
- School of Chemistry and Biosciences, University of Bradford , Bradford, West Yorkshire, U.K. , BD1 1DP
| | - C W Ian Douglas
- Dental School, University of Sheffield , 19 Claremont Crescent, Sheffield, South Yorkshire, U.K. , S10 2TA
| | - Joanna Shepherd
- Dental School, University of Sheffield , 19 Claremont Crescent, Sheffield, South Yorkshire, U.K. , S10 2TA
| | - Stephen Rimmer
- School of Chemistry and Biosciences, University of Bradford , Bradford, West Yorkshire, U.K. , BD1 1DP
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Otto S, Scholz N, Behnke T, Resch-Genger U, Heinze K. Thermo-Chromium: A Contactless Optical Molecular Thermometer. Chemistry 2017; 23:12131-12135. [DOI: 10.1002/chem.201701726] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Sven Otto
- Institute of Inorganic Chemistry and Analytical Chemistry; Johannes Gutenberg-University of Mainz; Duesbergweg 10-14 55128 Mainz Germany
- Graduate School Materials Science in Mainz; Staudingerweg 9 55128 Mainz Germany
| | - Norman Scholz
- Division 1.10; Federal Institute for Materials Research and Testing (BAM); Richard-Willstätter-Strasse 11 12489 Berlin Germany
| | - Thomas Behnke
- Division 1.10; Federal Institute for Materials Research and Testing (BAM); Richard-Willstätter-Strasse 11 12489 Berlin Germany
| | - Ute Resch-Genger
- Division 1.10; Federal Institute for Materials Research and Testing (BAM); Richard-Willstätter-Strasse 11 12489 Berlin Germany
| | - Katja Heinze
- Institute of Inorganic Chemistry and Analytical Chemistry; Johannes Gutenberg-University of Mainz; Duesbergweg 10-14 55128 Mainz Germany
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Bañuls MJ, Jiménez-Meneses P, Meyer A, Vasseur JJ, Morvan F, Escorihuela J, Puchades R, Maquieira Á. Improved Performance of DNA Microarray Multiplex Hybridization Using Probes Anchored at Several Points by Thiol-Ene or Thiol-Yne Coupling Chemistry. Bioconjug Chem 2017; 28:496-506. [PMID: 28042940 DOI: 10.1021/acs.bioconjchem.6b00624] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleic acid microarray-based assay technology has shown lacks in reproducibility, reliability, and analytical sensitivity. Here, a new strategy of probe attachment modes for silicon-based materials is built up. Thus, hybridization ability is enhanced by combining thiol-ene or thiol-yne click chemistry reactions with a multipoint attachment of polythiolated probes. The viability and performance of this approach was demonstrated by specifically determining Salmonella PCR products up to a 20 pM sensitivity level.
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Affiliation(s)
- Maria-Jose Bañuls
- Interuniversitary Research Institute for Molecular Recognition and Technological Development (IDM), Chemistry Department, Universitat Politècnica de València , Camino de Vera s/n, 46022 Valencia, Spain
| | - Pilar Jiménez-Meneses
- Interuniversitary Research Institute for Molecular Recognition and Technological Development (IDM), Chemistry Department, Universitat Politècnica de València , Camino de Vera s/n, 46022 Valencia, Spain
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier , ENSCM, place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier , ENSCM, place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - François Morvan
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier , ENSCM, place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Jorge Escorihuela
- Interuniversitary Research Institute for Molecular Recognition and Technological Development (IDM), Chemistry Department, Universitat Politècnica de València , Camino de Vera s/n, 46022 Valencia, Spain
| | - Rosa Puchades
- Interuniversitary Research Institute for Molecular Recognition and Technological Development (IDM), Chemistry Department, Universitat Politècnica de València , Camino de Vera s/n, 46022 Valencia, Spain
| | - Ángel Maquieira
- Interuniversitary Research Institute for Molecular Recognition and Technological Development (IDM), Chemistry Department, Universitat Politècnica de València , Camino de Vera s/n, 46022 Valencia, Spain
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32
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Ma Y, Dai X, Hong T, Munk GB, Libera M. A NASBA on microgel-tethered molecular-beacon microarray for real-time microbial molecular diagnostics. Analyst 2017; 142:147-155. [DOI: 10.1039/c6an02192a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Gel-tethered molecular beacons coupled with NASBA RNA amplification enable real-time microbial detection and differentiation in a bloodstream infection model.
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Affiliation(s)
- Y. Ma
- Dept of Chemical Engr & Materials Science
- Stevens Institute of Technology
- Hoboken
- USA
| | - X. Dai
- Dept of Chemical Engr & Materials Science
- Stevens Institute of Technology
- Hoboken
- USA
- Currently with Oxford Nanopore
| | - T. Hong
- Hackensack University Medical Center
- Hackensack
- USA
| | - G. B. Munk
- Hackensack University Medical Center
- Hackensack
- USA
| | - M. Libera
- Dept of Chemical Engr & Materials Science
- Stevens Institute of Technology
- Hoboken
- USA
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33
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Fidan Z, Wende A, Resch-Genger U. Visible and red emissive molecular beacons for optical temperature measurements and quality control in diagnostic assays utilizing temperature-dependent amplification reactions. Anal Bioanal Chem 2016; 409:1519-1529. [DOI: 10.1007/s00216-016-0088-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/31/2016] [Accepted: 11/07/2016] [Indexed: 12/11/2022]
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34
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MALDI-TOF mass spectrometry for the identification of lactic acid bacteria isolated from a French cheese: The Maroilles. Int J Food Microbiol 2016; 247:2-8. [PMID: 27423415 DOI: 10.1016/j.ijfoodmicro.2016.07.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 06/11/2016] [Accepted: 07/07/2016] [Indexed: 11/23/2022]
Abstract
In this study we identified the culturable population of mesophilic lactic acid bacteria (LAB) from a French cheese Maroilles made either with raw or pasteurized milk using MALDI-TOF mass spectrometry (MS). Samples from rind and heart of Maroilles cheese were used, the LAB were selected on MRS agar at 30°C and 197 Gram-positive and catalase-negative strains were subjected to identification by MALDI-TOF MS profiling. All strains were unambiguously identified: 105 strains from Maroilles made with raw milk (38 on the rind and 67 in the heart) and 92 strains from Maroilles made with pasteurized milk (39 on the rind and 53 in the heart). MALDI-TOF MS identification allowed identification of three genera belonging to LAB including Lactobacillus, Enterococcus and Leuconostoc. Lactobacillus was the most represented genus with seven species: Lactobacillus plantarum (L. plantarum), L. paracasei, L. curvatus, L. rhamnosus, L. fructivorans, L. parabuchneri, L. brevis found in Maroilles made with both kind of milk. The correlation between the 16S rDNA-based identification performed on selected strains and those obtained by MALDI-TOF-MS demonstrates that this fast, economically affordable, robust and reliable method for bacteria characterisation stands as an attractive alternative to the commonly-used methods and its application in food industry is discussed.
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Mandakovic D, Glasner B, Maldonado J, Aravena P, González M, Cambiazo V, Pulgar R. Genomic-Based Restriction Enzyme Selection for Specific Detection of Piscirickettsia salmonis by 16S rDNA PCR-RFLP. Front Microbiol 2016; 7:643. [PMID: 27242682 PMCID: PMC4860512 DOI: 10.3389/fmicb.2016.00643] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/18/2016] [Indexed: 12/24/2022] Open
Abstract
The gram negative facultative bacterium P. salmonis is the etiological agent of Salmonid Rickettsial Septicaemia (SRS), a severe disease that causes important economic losses in the global salmon farmer industry. Despite efforts to control this disease, the high frequency of new epizootic events indicate that the vaccine and antibiotics treatments have limited effectiveness, therefore the preventive and diagnostic approaches must be improved. A comparison of several methodologies for SRS diagnostic indicate differences in their specificity and its capacity to detect other bacteria coexisting with P. salmonis in culture media (contamination) and fish samples (coinfection), aspects relevant for research, vaccine development and clinical diagnostic. By computer-simulation analyses, we identified a group of restriction enzymes that generate unique P. salmonis 16S rDNA band patterns, distinguishable from all other bacteria. From this information, we designed and developed a PCR-RFLP (Polymerase Chain Reaction—Restriction Fragment Length Polymorphism) assay, which was validated using 16S rDNA universal primers and restriction enzyme PmaCI for the amplification and digestion, respectively. Experimental validation was performed by comparing the restriction pattern of P. salmonis with the restriction patterns generated by bacteria that cohabit with P. salmonis (fish bacterial isolates and culture media contaminants). Our results indicate that the restriction enzyme selection pipeline was suitable to design a more specific, sensible, faster and cheaper assay than the currently used P. salmonis detection methodologies.
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Affiliation(s)
- Dinka Mandakovic
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Fondap Center for Genoma RegulationSantiago, Chile
| | - Benjamín Glasner
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Fondap Center for Genoma RegulationSantiago, Chile
| | - Pamela Aravena
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Laboratorio de Genómica Aplicada, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Fondap Center for Genoma RegulationSantiago, Chile; Laboratorio de Genómica Aplicada, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Fondap Center for Genoma RegulationSantiago, Chile; Laboratorio de Genómica Aplicada, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile; Fondap Center for Genoma RegulationSantiago, Chile; Laboratorio de Genómica Aplicada, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de ChileSantiago, Chile
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Noyer C, Abot A, Trouilh L, Leberre VA, Dreanno C. Phytochip: development of a DNA-microarray for rapid and accurate identification of Pseudo-nitzschia spp and other harmful algal species. J Microbiol Methods 2015; 112:55-66. [PMID: 25765159 DOI: 10.1016/j.mimet.2015.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 10/23/2022]
Abstract
Detection of harmful algal blooms has become a challenging concern because of the direct impacts on public health and economy. The identification of toxic dinoflagellates and diatoms in monitoring programs requires an extensive taxonomic expertise and is time consuming. Advances in molecular biology have allowed the development of new approaches, more rapid, accurate and cost-effective for detecting these microorganisms. In this context, we developed a new DNA microarray (called, Phytochip) for the simultaneous detection of multiple HAB species with a particular emphasis on Pseudo-nitzschia species. Oligonucleotide probes were designed along the rRNA operon. After DNA extraction, the target rDNA genes were amplified and labeled using an asymmetric PCR; then, the amplicons were hybridized to the oligonucleotide probes present on the chips. The total assay from seawater sampling to data acquisition can be performed within a working day. Specificity and sensitivity were assessed by using monoclonal cultures, mixtures of species and field samples spiked with a known amount of cultured cells. The Phytochip with its 81 validated oligonucleotide probes was able to detect 12 species of Pseudo-nitzschia and 11 species of dinoflagellates among which were 3 species of Karenia and 3 species of Alexandrium. The Phytochip was applied to environmental samples already characterized by light microscopy and cloned into DNA libraries. The hybridizations on the Phytochip were in good agreement with the sequences retrieved from the clone libraries and the microscopic observations. The Phytochip enables a reliable multiplex detection of phytoplankton and can assist a water quality monitoring program as well as more general ecological research.
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Affiliation(s)
- Charlotte Noyer
- IFREMER, Centre Bretagne, Laboratoire Detections, Capteurs et Mesures, F-29280 Plouzané, France; Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Anne Abot
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Lidwine Trouilh
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Véronique Anton Leberre
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France; CNRS, UMR5504, F-31400 Toulouse, France
| | - Catherine Dreanno
- IFREMER, Centre Bretagne, Laboratoire Detections, Capteurs et Mesures, F-29280 Plouzané, France.
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