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Madadelahi M, Agarwal R, Martinez-Chapa SO, Madou MJ. A roadmap to high-speed polymerase chain reaction (PCR): COVID-19 as a technology accelerator. Biosens Bioelectron 2024; 246:115830. [PMID: 38039729 DOI: 10.1016/j.bios.2023.115830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
The limit of detection (LOD), speed, and cost of crucial COVID-19 diagnostic tools, including lateral flow assays (LFA), enzyme-linked immunosorbent assays (ELISA), and polymerase chain reactions (PCR), have all improved because of the financial and governmental support for the epidemic. The most notable improvement in overall efficiency among them has been seen with PCR. Its significance for human health increased during the COVID-19 pandemic, when it emerged as the commonly used approach for identifying the virus. However, because of problems with speed, complexity, and expense, PCR deployment in point-of-care settings continues to be difficult. Microfluidic platforms offer a promising solution by enabling the development of smaller, more affordable, and faster PCR systems. In this review, we delve into the engineering challenges associated with the advancement of high-speed microfluidic PCR equipment. We introduce criteria that facilitate the evaluation and comparison of factors such as speed, LOD, cycling efficiency, and multiplexing capacity, considering sample volume, fluidics, PCR reactor geometry and materials, as well as heating/cooling methods. We also provide a comprehensive list of commercially available PCR devices and conclude with projections and a discussion regarding the current obstacles that need to be addressed in order to progress further in this field.
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Affiliation(s)
- Masoud Madadelahi
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, 64849, NL, Mexico; Department of Mechanical Engineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Rahul Agarwal
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, 64849, NL, Mexico
| | | | - Marc J Madou
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, 64849, NL, Mexico; Autonomous Medical Devices Incorporated (AMDI), Santa Ana, CA, 92704, USA.
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2
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Goyal PA, Bankar NJ, Mishra VH, Borkar SK, Makade JG. Revolutionizing Medical Microbiology: How Molecular and Genomic Approaches Are Changing Diagnostic Techniques. Cureus 2023; 15:e47106. [PMID: 38022057 PMCID: PMC10646819 DOI: 10.7759/cureus.47106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Molecular and genomic approaches have revolutionized medical microbiology by offering faster and more accurate diagnostic techniques for infectious diseases. Traditional methods, which include culturing microbes and biochemical testing, are time-consuming and may not detect antibiotic-resistant strains. In contrast, molecular and genomic methods, including polymerase chain reaction (PCR)-based techniques and whole-genome sequencing, provide rapid and precise detection of pathogens, early-stage diseases, and antibiotic-resistant strains. These approaches have advantages such as high sensitivity and specificity, the potential for targeted therapies, and personalized medicine. However, implementing molecular and genomic techniques faces challenges related to cost, equipment, expertise, and data analysis. Ethical and legal considerations regarding patient privacy and genetic data usage also arise. Nonetheless, the future of medical microbiology lies in the widespread adoption of molecular and genomic approaches, which can lead to improved patient outcomes and the identification of antibiotic-resistant strains. Continued advancements, education, and exploration of ethical implications are necessary to fully harness the potential of molecular and genomic techniques in medical microbiology.
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Affiliation(s)
- Poyasha A Goyal
- Microbiology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Nandkishor J Bankar
- Microbiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Vaishnavi H Mishra
- Microbiology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Sonali K Borkar
- Community Medicine, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research (DU), Wardha, IND
| | - Jagadish G Makade
- Community Medicine, Datta Meghe Medical College, Datta Meghe Institute of Medical Sciences(DU), Wardha, IND
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Nouwairi RL, Cunha LL, Turiello R, Scott O, Hickey J, Thomson S, Knowles S, Chapman JD, Landers JP. Ultra-rapid real-time microfluidic RT-PCR instrument for nucleic acid analysis. LAB ON A CHIP 2022; 22:3424-3435. [PMID: 35959772 PMCID: PMC9474628 DOI: 10.1039/d2lc00495j] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The polymerase chain reaction (PCR) is paramount in nucleic acid amplification testing, and for many assays, the use of PCR or qPCR is considered the 'gold standard'. While instrumentation for executing PCR has advanced over the last two decades, a growing interest in point-of-need testing has highlighted the deficit that exists for 'rapid PCR' systems. Here, we describe a field-forward prototype instrument capable of ultra-fast thermal cycling for real-time PCR amplification of DNA and RNA. The custom-designed, injection-molded microfluidic chips interface with a novel mechatronic system to complete 40 cycles of real-time PCR in under 10 minutes, an 84% reduction in time compared to a standard 50 minute assay. Such rapid amplification is enabled by two thermoelectric Peltiers capable of efficiently heating and cooling the sample at 12 and 10 °C s-1, respectively. Judicious selection and strategic placement of the thermal cyclers and fluorescence detector relative to the microchip enable synchronized thermal cycling and fluorescence monitoring, further reducing time-to-result. Robust amplification and detection of DNA and RNA targets empowers laboratories to achieve rapid, actionable information in endless applications.
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Affiliation(s)
| | | | | | | | | | | | | | | | - James P Landers
- University of Virginia, USA.
- MicroGEM International, PLC, USA
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4
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Ota Y, Okada R, Takahashi H, Saito R. Molecular detection of fluoroquinolone-resistant Neisseria meningitidis by using mismatched PCR-restriction fragment length polymorphism technique. Front Cell Infect Microbiol 2022; 12:911911. [PMID: 35982783 PMCID: PMC9378782 DOI: 10.3389/fcimb.2022.911911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ciprofloxacin (CIP) is a commonly used antibiotic for meningococcal chemoprophylaxis, and the mutations in the quinolone resistance-determining region of gyrA are associated with CIP-resistant Neisseria meningitidis. Here, we established a mismatched PCR-restriction fragment length polymorphism (RFLP) assay to detect a mutation at codon 91 of gyrA, followed by high-level CIP-resistant meningococci. We designed PCR-RFLP primers to detect the T91I mutation in gyrA by introducing an artificial AciI cleavage site. This assay was performed using 26 N. meningitidis strains whose gyrA sequences have been characterized. The amplified 160 bp PCR product from gyrA was digested into three fragments (80, 66, and 14 bp) when there was no mutation, or two fragments (146 and 14 bp) when there was a mutation at codon 91. A correlation was observed between the mismatched PCR-RFLP assay and gyrA sequencing. This rapid, simple, and accurate assay has the potential to detect CIP-resistant N. meningitidis in clinical microbiology laboratories, contributing to the appropriate antibiotic selection for meningococcal chemoprophylaxis, will help maintain an effective treatment for close contacts of IMD patients, and prevent the spread of CIP-resistant N. meningitidis.
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Affiliation(s)
- Yusuke Ota
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Reina Okada
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hideyuki Takahashi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
- *Correspondence: Ryoichi Saito,
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Cunha ML, da Silva SS, Stracke MC, Zanette DL, Aoki MN, Blanes L. Sample Preparation for Lab-on-a-Chip Systems in Molecular Diagnosis: A Review. Anal Chem 2021; 94:41-58. [PMID: 34870427 DOI: 10.1021/acs.analchem.1c04460] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rapid and low-cost molecular analysis is especially required for early and specific diagnostics, quick decision-making, and sparing patients from unnecessary tests and hospitals from extra costs. One way to achieve this objective is through automated molecular diagnostic devices. Thus, sample-to-answer microfluidic devices are emerging with the promise of delivering a complete molecular diagnosis system that includes nucleic acid extraction, amplification, and detection steps in a single device. The biggest issue in such equipment is the extraction process, which is normally laborious and time-consuming but extremely important for sensitive and specific detection. Therefore, this Review focuses on automated or semiautomated extraction methodologies used in lab-on-a-chip devices. More than 15 different extraction methods developed over the past 10 years have been analyzed in terms of their advantages and disadvantages to improve extraction procedures in future studies. Herein, we are able to explain the high applicability of the extraction methodologies due to the large variety of samples in which different techniques were employed, showing that their applications are not limited to medical diagnosis. Moreover, we are able to conclude that further research in the field would be beneficial because the methodologies presented can be affordable, portable, time efficient, and easily manipulated, all of which are strong qualities for point-of-care technologies.
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Affiliation(s)
- Mylena Lemes Cunha
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Stella Schuster da Silva
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Mateus Cassaboni Stracke
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010.,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010.,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil 81350-010
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Dong X, Liu L, Tu Y, Zhang J, Miao G, Zhang L, Ge S, Xia N, Yu D, Qiu X. Rapid PCR powered by microfluidics: A quick review under the background of COVID-19 pandemic. Trends Analyt Chem 2021; 143:116377. [PMID: 34188341 PMCID: PMC8223007 DOI: 10.1016/j.trac.2021.116377] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
PCR has been widely used in different fields including molecular biology, pathogen detection, medical diagnosis, food detection and etc. However, the difficulty of promoting PCR in on-site point-of-care testing reflects on challenges relative to its speed, convenience, complexity, and even cost. With the emerging state-of-art of microfluidics, rapid PCR can be achieved with more flexible ways in micro-reactors. PCR plays a critical role in the detection of SARS-CoV-2. Under this special background of COVID-19 pandemic, this review focuses on the latest rapid microfluidic PCR. Rapid PCR is concluded in two main features, including the reactor (type, size, material) and the implementation of thermal cycling. Especially, the compromise between speed and sensitivity with microfluidic PCR is explored based on the system ratio of (thermal cycling time)/(reactor size). Representative applications about the detection of pathogens and SARS-CoV-2 viruses based on rapid PCR or other isothermal amplification are discussed as well.
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Affiliation(s)
- Xiaobin Dong
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Luyao Liu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yunping Tu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jing Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029, China
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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