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Chen Y, Peng J, Zhu Z, Zhang W, Wang L, Xu J, Liu Q, Liu J. Development of a highly specific LAMP assay for detection of Sarcocystis tenella and Sarcocystis gigantea in sheep. Parasitol Res 2024; 123:324. [PMID: 39276229 DOI: 10.1007/s00436-024-08349-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/06/2024] [Indexed: 09/16/2024]
Abstract
Sarcocystis infection in sheep has caused significant economic losses in the livestock industry, and the genetic similarity among Sarcocystis species highlights the need for precise diagnostic methods in sheep. This study developed a loop-mediated isothermal amplification (LAMP) method targeting COX-1 and 28S rRNA genes to detect Sarcocystis tenella and Sarcocystis gigantea, respectively. The LAMP method exhibited high specificity, selectively amplifying target DNA sequences without cross-reactivity with closely related protozoa, such as Toxoplasma gondii and Neospora caninum. Detection limits were determined as 3 × 105 copies/L for S. tenella and 6 × 104 copies/L for S. gigantea, enabling sensitive identification of low-level infections. Comparative analysis with conventional PCR on sheep cardiac tissues demonstrated a higher LAMP detection rate (80.0% vs 66.7%). In conclusion, the LAMP method offers superior sensitivity to conventional PCR, allows visual confirmation of results, and provides a rapid diagnostic tool for identifying S. tenella and S. gigantea infection in sheep. However, due to the limitation of sample availability, we were unable to assess all Sarcocystis species that use sheep as intermediate hosts, which warrants further research.
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Affiliation(s)
- Yajie Chen
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jing Peng
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Zifu Zhu
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Wen Zhang
- Beijing General Station of Animal Husbandry, Beijing, 100110, People's Republic of China
| | - Lifang Wang
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jianhai Xu
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Qun Liu
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jing Liu
- National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People's Republic of China.
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Shi J, Ding S, Li C, Chen G, Du F, Wang S, Yue A, Ren K, Yang Z, Xu P, Dong J, Zhao J, Tang Z. Ultrafast DNA detection based on turn-back loop primer-accelerated LAMP (TLAMP). Anal Chim Acta 2024; 1321:343041. [PMID: 39155098 DOI: 10.1016/j.aca.2024.343041] [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: 03/07/2024] [Revised: 07/08/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024]
Abstract
Rapid DNA detection is a long-pursuing goal in molecular detection, especially in combating infectious diseases. Loop-mediated isothermal amplification (LAMP) is a robust and prevailing DNA detection method in pathogen detection, which has been drawing broad interest in improving its performance. Herein, we reported a new strategy and developed a new LAMP variant named TLAMP with a superior amplification rate. In this strategy, the turn-back loop primers (TLPs) were devised by ingeniously extending the 5' end of the original loop primer, which conferred the new role of being the inner primer for TLPs while retaining its original function as the loop primer. In theory, based on the bifunctional TLPs, a total of eight basic dumbbell-like structures and four cyclic amplification pathways were produced to significantly enhance the amplification efficiency of TLAMP. With the enhancing effect of TLPs, TLAMP exhibited a significantly reduced amplification-to-result time compared to the conventional six-primer LAMP (typically 1 h), enabling rapid DNA detection within 20 min. Furthermore, TLAMP proved to be about 10 min faster than the fast LAMP variants reported so far, while still presenting comparable sensitivity and higher repeatability. Finally, TLAMP successfully achieved an ultrafast diagnosis of Monkeypox virus (MPXV), capable of detecting as few as 10 copies (0.67copies/μL) of pseudovirus within 20 min using real-time fluorescence assay or within 30 min using a colorimetric assay, suggesting that the proposed TLAMP offers a sensitive, specific, reliable, and, most importantly, ultrafast DNA detection method when facing the challenges posed by infectious diseases.
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Affiliation(s)
- Jinyi Shi
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China; Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Sheng Ding
- School of Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610052, PR China
| | - Chen Li
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Sifan Wang
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Aiqin Yue
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Kaiyuan Ren
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Zhirong Yang
- People's Hospital of De Yang City, Deyang, 618099, PR China
| | - Pei Xu
- People's Hospital of De Yang City, Deyang, 618099, PR China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Jinzhong Zhao
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China.
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
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3
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Feddema JJ, Fernald KDS, Keijser BJF, Kieboom J, van de Burgwal LHM. Commercial Opportunity or Addressing Unmet Needs-Loop-Mediated Isothermal Amplification (LAMP) as the Future of Rapid Diagnostic Testing? Diagnostics (Basel) 2024; 14:1845. [PMID: 39272630 PMCID: PMC11394392 DOI: 10.3390/diagnostics14171845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 09/15/2024] Open
Abstract
Loop-Mediated Isothermal Amplification (LAMP) technology is emerging as a rapid pathogen testing method, potentially challenging the RT-PCR "gold standard". Despite recent advancements, LAMP's widespread adoption remains limited. This study provides a comprehensive market overview and assesses future growth prospects to aid stakeholders in strategic decision-making and policy formulation. Using a dataset of 1134 LAMP patent documents, we analyzed lifecycle and geographic distribution, applicant profiles, CPC code classifications, and patent claims. Additionally, we examined clinical developments from 21 curated clinical trials, focusing on trends, geographic engagement, sponsor types, and the conditions and pathogens investigated. Our analysis highlights LAMP's potential as a promising rapid pathogen testing alternative, especially in resource-limited areas. It also reveals a gap between clinical research, which targets bacterial and parasitic diseases like malaria, leishmaniasis, and tuberculosis, and basic research and commercial efforts that prioritize viral diseases such as SARS-CoV-2 and influenza. European stakeholders emphasize the societal impact of addressing unmet needs in resource-limited areas, while American and Asian organizations focus more on research, innovation, and commercialization.
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Affiliation(s)
- Jelle J Feddema
- Athena Institute, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Kenneth D S Fernald
- Athena Institute, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Bart J F Keijser
- TNO Healthy Living and Work, Microbiology and Systems Biology, Sylviusweg 71, 2333 BE Leiden, The Netherlands
| | - Jasper Kieboom
- TNO Healthy Living and Work, Microbiology and Systems Biology, Sylviusweg 71, 2333 BE Leiden, The Netherlands
| | - Linda H M van de Burgwal
- Athena Institute, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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Flores-Contreras EA, González-González E, Trujillo-Rodríguez GDJ, Rodríguez-Sánchez IP, Ancer-Rodríguez J, Pérez-Maya AA, Alvarez-Cuevas S, Martinez-Fierro ML, Marino-Martínez IA, Garza-Veloz I. Isothermal Technologies for HPV Detection: Current Trends and Future Perspectives. Pathogens 2024; 13:653. [PMID: 39204253 PMCID: PMC11357395 DOI: 10.3390/pathogens13080653] [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: 06/16/2024] [Revised: 07/12/2024] [Accepted: 07/25/2024] [Indexed: 09/03/2024] Open
Abstract
The human papillomavirus (HPV) is a non-enveloped DNA virus transmitted through skin-to-skin contact that infects epithelial and mucosal tissue. It has over 200 known genotypes, classified by their pathogenicity as high-risk and low-risk categories. High-risk HPV genotypes are associated with the development of different types of cancers, including cervical cancer, which is a leading cause of mortality in women. In clinical practice and the market, the principal tests used to detect HPV are based on cytology, hybrid detection, and qPCR. However, these methodologies may not be ideal for the required timely diagnosis. Tests have been developed based on isothermal nucleic acid amplification tests (INAATs) as alternatives. These tests offer multiple advantages over the qPCR, such as not requiring specialized laboratories, highly trained personnel, or expensive equipment like thermocyclers. This review analyzes the different INAATs applied for the detection of HPV, considering the specific characteristics of each test, including the HPV genotypes, gene target, the limit of detection (LOD), detection methods, and detection time. Additionally, we discuss the tests available on the market that are approved by the Food and Drug Administration (FDA). Finally, we address the challenges and potential solutions for the large-scale implementation of INAATs, particularly in rural or underserved areas.
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Affiliation(s)
- Elda A. Flores-Contreras
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Everardo González-González
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Gerardo de Jesús Trujillo-Rodríguez
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Iram P. Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico;
| | - Jesús Ancer-Rodríguez
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Antonio Alí Pérez-Maya
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico;
| | - Salomon Alvarez-Cuevas
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Margarita L. Martinez-Fierro
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
| | - Iván A. Marino-Martínez
- Departamento de Patología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Francisco I. Madero y Dr. E. Aguirre Pequeño s/n, Mitras Centro, Monterrey 64460, Mexico; (E.A.F.-C.); (J.A.-R.); (S.A.-C.)
| | - Idalia Garza-Veloz
- Molecular Medicine Laboratory, Unidad Académica de Medicina Humana y Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas 98160, Mexico; (E.G.-G.); (G.d.J.T.-R.); (M.L.M.-F.)
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5
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Chen Z, Luo G, Ren J, Wang Q, Zhao X, Wei L, Wang Y, Liu Y, Deng Y, Li S. Recent Advances in and Application of Fluorescent Microspheres for Multiple Nucleic Acid Detection. BIOSENSORS 2024; 14:265. [PMID: 38920569 PMCID: PMC11201543 DOI: 10.3390/bios14060265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Traditional single nucleic acid assays can only detect one target while multiple nucleic acid assays can detect multiple targets simultaneously, providing comprehensive and accurate information. Fluorescent microspheres in multiplexed nucleic acid detection offer high sensitivity, specificity, multiplexing, flexibility, and scalability advantages, enabling precise, real-time results and supporting clinical diagnosis and research. However, multiplexed assays face challenges like complexity, costs, and sample handling issues. The review explores the recent advancements and applications of fluorescent microspheres in multiple nucleic acid detection. It discusses the versatility of fluorescent microspheres in various fields, such as disease diagnosis, drug screening, and personalized medicine. The review highlights the possibility of adjusting the performance of fluorescent microspheres by modifying concentrations and carrier forms, allowing for tailored applications. It emphasizes the potential of fluorescent microsphere technology in revolutionizing nucleic acid detection and advancing health, disease treatment, and medical research.
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Affiliation(s)
- Zhu Chen
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Gaoming Luo
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Jie Ren
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Qixuan Wang
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Hunan Engineering Research Center for Early Diagnosis and Treatment of Liver Cancer, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xinping Zhao
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Linyu Wei
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
- Institute of Cytology and Genetics, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Yue Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China;
| | - Yuan Liu
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Yan Deng
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
| | - Song Li
- MOE Key Lab of Rare Pediatric Diseases & Hengyang Medical School, University of South China, Hengyang 421001, China; (G.L.); (J.R.); (Q.W.); (X.Z.); (L.W.); (Y.L.); (Y.D.)
- Institute for Future Sciences, University of South China, Changsha 410008, China
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Brandolini M, Grumiro L, Farabegoli P, Dirani G, Zannoli S, Zaghi I, Guerra M, Taddei F, Gatti G, Marzucco A, Montanari MS, De Pascali AM, Semprini S, Cricca M, Sambri V. Evaluation of a rapid Loop Mediated Isothermal Amplification (LAMP) test for the laboratory diagnosis of sexually transmitted infections. PLoS One 2024; 19:e0298398. [PMID: 38512825 PMCID: PMC10956856 DOI: 10.1371/journal.pone.0298398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
Sexually transmitted infections (STIs) have seen a considerable increase in the last years and given the health burden they may represent from both a personal and community perspective, they require surveillance and prevention programmes based on a timely and decentralized diagnosis. In this context, user-friendly rapid molecular tests may represent a good trade-off between diagnostic accuracy, accessibility and affordability. In this study we evaluated the diagnostic performance of a new real-time LAMP (Loop Mediated Isothermal Amplification) method for the rapid detection and differentiation of 7 major sexually transmissible pathogens by analysing real clinical samples (genital and extra-genital matrices) from individuals with suspected STIs. The assay showed good overall diagnostic performances in terms of sensitivity, specificity and concordance with a gold-standard PCR-based molecular method. This assay, not requiring specialised laboratory technicians or expensive instrumentation, but nonetheless capable of guaranteeing accurate results, is within the reach of outpatient settings, obstetrics, and gynaecology clinic, hence ensuring on-field access to early diagnosis.
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Affiliation(s)
- Martina Brandolini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Laura Grumiro
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Patrizia Farabegoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Giorgio Dirani
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Silvia Zannoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Irene Zaghi
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Unit of Infectious Diseases, Santa Maria delle Croci Hospital, Ravenna, Italy
| | - Massimiliano Guerra
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Francesca Taddei
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Giulia Gatti
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Anna Marzucco
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | | | - Alessandra Mistral De Pascali
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Simona Semprini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
| | - Monica Cricca
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, Cesena, Italy
- Department Medical and Surgical Sciences (DIMEC)—Alma Mater Studiorum, University of Bologna, Bologna, Italy
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7
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Omar RF, Boissinot M, Huletsky A, Bergeron MG. Tackling Infectious Diseases with Rapid Molecular Diagnosis and Innovative Prevention. Infect Dis Rep 2024; 16:216-227. [PMID: 38525764 PMCID: PMC10961803 DOI: 10.3390/idr16020017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024] Open
Abstract
Infectious diseases (IDs) are a leading cause of death. The diversity and adaptability of microbes represent a continuing risk to health. Combining vision with passion, our transdisciplinary medical research team has been focussing its work on the better management of infectious diseases for saving human lives over the past five decades through medical discoveries and innovations that helped change the practice of medicine. The team used a multiple-faceted and integrated approach to control infectious diseases through fundamental discoveries and by developing innovative prevention tools and rapid molecular diagnostic tests to fulfill the various unmet needs of patients and health professionals in the field of ID. In this article, as objectives, we put in context two main research areas of ID management: innovative infection prevention that is woman-controlled, and the rapid molecular diagnosis of infection and resistance. We also explain how our transdisciplinary approach encompassing specialists from diverse fields ranging from biology to engineering was instrumental in achieving success. Furthermore, we discuss our vision of the future for translational research to better tackle IDs.
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Affiliation(s)
- Rabeea F. Omar
- Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC G1V 4G2, Canada; (M.B.); (A.H.); (M.G.B.)
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8
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Ngoc LTN, Lee YC. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. BIOSENSORS 2024; 14:97. [PMID: 38392016 PMCID: PMC10886876 DOI: 10.3390/bios14020097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Ribonucleic acid (RNA) viruses are one of the major classes of pathogens that cause human diseases. The conventional method to detect RNA viruses is real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), but it has some limitations. It is expensive and time-consuming, with infrastructure and trained personnel requirements. Its high throughput requires sophisticated automation and large-scale infrastructure. Isothermal amplification methods have been explored as an alternative to address these challenges. These methods are rapid, user-friendly, low-cost, can be performed in less specialized settings, and are highly accurate for detecting RNA viruses. Microfluidic technology provides an ideal platform for performing virus diagnostic tests, including sample preparation, immunoassays, and nucleic acid-based assays. Among these techniques, nucleic acid isothermal amplification methods have been widely integrated with microfluidic platforms for RNA virus detection owing to their simplicity, sensitivity, selectivity, and short analysis time. This review summarizes some common isothermal amplification methods for RNA viruses. It also describes commercialized devices and kits that use isothermal amplification techniques for SARS-CoV-2 detection. Furthermore, the most recent applications of isothermal amplification-based microfluidic platforms for RNA virus detection are discussed in this article.
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Affiliation(s)
- Le Thi Nhu Ngoc
- Department of Nano Science and Technology Convergence, Gachon University, 1342 Seongnam-Daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
| | - Young-Chul Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
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9
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Yang H, Liu A, Ma F, Gao X, Wang K, Wang Y. Establishment of portable Pseudomonas aeruginosa detection platform based on one-tube CRISPR/Cas12a combined with recombinase polymerase amplification technology. Clin Chim Acta 2024; 554:117760. [PMID: 38176521 DOI: 10.1016/j.cca.2024.117760] [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: 11/01/2023] [Revised: 12/07/2023] [Accepted: 01/01/2024] [Indexed: 01/06/2024]
Abstract
Pseudomonas aeruginosa, a common Gram-negative bacterium, is associated with diverse diseases. Its increasing resistance to antibiotics presents challenges in clinical treatment. The predominant diagnostic approach involves conventional biochemical cultures, known for their time and labor intensiveness. Despite progress in isothermal amplification studies, limitations persist, including reliance on specialized equipment, intricate primer design, and aerosol contamination. Therefore, there is a demand for enhanced clinical assays. This study successfully combined RPA and CRISPR/Cas12a techniques. Through a series of experiments involving the design and screening of lasB crRNA, the creation of lasB RPA primers, and the establishment of a streamlined RPA-CRISPR/Cas12a assay, the study developed a one-tube detection method targeting P. aeruginosa's lasB gene. The assay demonstrated inclusive behavior across standard and 21 isolates, while specifically discerning P. aeruginosa from diverse strains. Sensitivity reached 15.9 CFU/reaction. Clinical validation revealed a 97.62% concordance with traditional methods. The one-tube assay's protocol mitigated aerosol contamination. Offering precision, specificity, and sensitivity, this method shows promise for field applications in resource-scarce regions, enabling early detection and improved management of P. aeruginosa infections.
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Affiliation(s)
- Haitao Yang
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Aibo Liu
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Fenfen Ma
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China
| | - Xuzhu Gao
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China
| | - Kun Wang
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China
| | - Yan Wang
- Department of Medicine Laboratory, The Second People's Hospital of Lianyungang Affiliated to Kangda College of Nanjing Medical University, The Second People's Hospital of Lianyungang City, Lianyungang 222000, China.
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10
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Ray SK, Mukherjee S. Innovation and Patenting Activities During COVID-19 and Advancement of Biochemical and Molecular Diagnosis in the Post- COVID-19 Era. Recent Pat Biotechnol 2024; 18:210-226. [PMID: 37779409 DOI: 10.2174/0118722083262217230921042127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/13/2023] [Accepted: 07/30/2023] [Indexed: 10/03/2023]
Abstract
The COVID-19 pandemic is to escalate globally and acquire new mutations quickly, so accurate diagnostic technologies play a vital role in controlling and understanding the epidemiology of the disease. A plethora of technologies acquires diagnosis of individuals and informs clinical management of COVID. Some important biochemical parameters for COVID diagnosis are the elevation of liver enzymes, creatinine, and nonspecific inflammatory markers such as C-reactive protein (CRP) and Interleukin 6 (IL-6). The main progression predictors are lymphopenia, elevated D-dimer, and hyperferritinemia, although it is also necessary to consider LDH, CPK, and troponin in the marker panel of diagnosis. Owing to the greater sensitivity and accuracy, molecular technologies such as conventional polymerase chain reaction (PCR), reverse transcription (RT)-PCR, nested PCR, loop-mediated isothermal amplification (LAMP), and xMAP technology have been extensively used for COVID diagnosis for some time now. To make so many diagnostics accessible to general people, many techniques may be exploited, including point of care (POC), also called bedside testing, which is developing as a portable promising tool in pathogen identification. Some other lateral flow assay (LFA)-centered techniques like SHERLOCK, CRISPR-Cas12a (AIOD-CRISPR), and FNCAS9 editor limited uniform detection assay (FELUDA), etc. have shown auspicious results in the rapid detection of pathogens. More recently, low-cost sequencing and advancements in big data management have resulted in a slow but steady rise of next-generation sequencing (NGS)-based approaches for diagnosis that have potential relevance for clinical purposes and may pave the way toward a better future. Due to the COVID-19 pandemic, various institutions provided free, specialized websites and tools to promote research and access to critically needed advanced solutions by alleviating research and analysis of data within a substantial body of scientific and patent literature regarding biochemical and molecular diagnosis published since January 2020. This circumstance is unquestionably unique and difficult for anyone using patent information to find pertinent disclosures at a specific date in a trustworthy manner.
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Affiliation(s)
- Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh-462020, India
| | - Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
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11
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Vloemans D, Van Hileghem L, Ordutowski H, Dal Dosso F, Spasic D, Lammertyn J. Self-Powered Microfluidics for Point-of-Care Solutions: From Sampling to Detection of Proteins and Nucleic Acids. Methods Mol Biol 2024; 2804:3-50. [PMID: 38753138 DOI: 10.1007/978-1-0716-3850-7_1] [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: 05/21/2024]
Abstract
Self-powered microfluidics presents a revolutionary approach to address the challenges of healthcare in decentralized and point-of-care settings where limited access to resources and infrastructure prevails or rapid clinical decision-making is critical. These microfluidic systems exploit physical and chemical phenomena, such as capillary forces and surface tension, to manipulate tiny volumes of fluids without the need for external power sources, making them cost-effective and highly portable. Recent technological advancements have demonstrated the ability to preprogram complex multistep liquid operations within the microfluidic circuit of these standalone systems, which enabled the integration of sensitive detection and readout principles. This chapter first addresses how the accessibility to in vitro diagnostics can be improved by shifting toward decentralized approaches like remote microsampling and point-of-care testing. Next, the crucial role of self-powered microfluidic technologies to enable this patient-centric healthcare transition is emphasized using various state-of-the-art examples, with a primary focus on applications related to biofluid collection and the detection of either proteins or nucleic acids. This chapter concludes with a summary of the main findings and our vision of the future perspectives in the field of self-powered microfluidic technologies and their use for in vitro diagnostics applications.
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Affiliation(s)
- Dries Vloemans
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | | | - Henry Ordutowski
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | | | - Dragana Spasic
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium.
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12
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Huang S, Wang X, Chen X, Liu X, Xu Q, Zhang L, Huang G, Wu J. Rapid and sensitive detection of Pseudomonas aeruginosa by isothermal amplification combined with Cas12a-mediated detection. Sci Rep 2023; 13:19199. [PMID: 37932335 PMCID: PMC10628258 DOI: 10.1038/s41598-023-45766-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
CRISPR based technologies have been used for fast and sensitive detection of pathogens. To test the possibility of CRISPR based detection strategy in Pseudomonas aeruginosa infections, a combined method of recombinase polymerase amplification followed by Cas12a-mediated detection via fluorescence reader or lateral flow biosensor (named Cas12a-RCFL) has been established in this study. The Cas12a-RCFL can detect as low as 50 CFU/mL Pseudomonas aeruginosa. The whole detection process can be finished within one hour with satisfied detection specificity. Cas12a-RCFL also shows good sensitivity of detecting Pseudomonas aeruginosa inStaphylococcus aureus and Acinetobacter baumannii contaminated samples. For the detection of 22 clinical samples, Cas12a-RCFL matches with PCR sequencing result exactly without DNA purification. This Cas12a-RCFL is rapid and sensitive with low cost, which shows good quality to be adopted as a point-of-care testing method.
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Affiliation(s)
- Siyi Huang
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Xianfeng Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, China
| | - Xinchong Chen
- Department of Burn and Plastic Surgery, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China
| | - Xiaoyu Liu
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Qiuqing Xu
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Lijun Zhang
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China
| | - Guangtao Huang
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
| | - Jun Wu
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, China.
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13
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Jiang K, Lee JH, Fung TS, Wu J, Liu C, Mi H, Rajapakse RPVJ, Balasuriya UBR, Peng YK, Go YY. Next-generation diagnostic test for dengue virus detection using an ultrafast plasmonic colorimetric RT-PCR strategy. Anal Chim Acta 2023; 1274:341565. [PMID: 37455070 DOI: 10.1016/j.aca.2023.341565] [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: 04/13/2023] [Revised: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023]
Abstract
The current global COVID-19 pandemic once again highlighted the urgent need for a simple, cost-effective, and sensitive diagnostic platform that can be rapidly developed for distribution and easy access in resource-limited areas. Here, we present a simple and low-cost plasmonic photothermal (PPT)-reverse transcription-colorimetric polymerase chain reaction (RTcPCR) for molecular diagnosis of dengue virus (DENV) infection. The assay can be completed within 54 min with an estimated detection limit of 1.6 copies/μL of viral nucleic acid. The analytical sensitivity and specificity of PPT-RTcPCR were comparable to that of the reference RT-qPCR assay. Moreover, the clinical performance of PPT-RTcPCR was evaluated and validated using 158 plasma samples collected from patients suspected of dengue infection. The results showed a diagnostic agreement of 97.5% compared to the reference RT-qPCR and demonstrated a clinical sensitivity and specificity of 97.0% and 100%, respectively. The simplicity and reliability of our PPT-RTcPCR strategy suggest it can provide a foundation for developing a field-deployable diagnostic assay for dengue and other infectious diseases.
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Affiliation(s)
- Kunlun Jiang
- Department of Chemistry, College of Science, City University of Hong Kong, Kowloon, 999077, Hong Kong, China
| | - Jung-Hoon Lee
- Department of Chemistry, Soonchunhyang University, Asan, 31538, South Korea.
| | - To Sing Fung
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong, China
| | - Jingrui Wu
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Congnuan Liu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong, China
| | - Hua Mi
- Department of Chemistry, College of Science, City University of Hong Kong, Kowloon, 999077, Hong Kong, China
| | - R P V Jayanthe Rajapakse
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, USA; Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Yung-Kang Peng
- Department of Chemistry, College of Science, City University of Hong Kong, Kowloon, 999077, Hong Kong, China.
| | - Yun Young Go
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong, China.
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14
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Lee JE, Toushik SH, Park HJ, Kim SA, Shim WB. Rapid detection of Shiga-toxin-producing Escherichia coli O157:H7 based on a colorimetric loop-mediated isothermal amplification (cLAMP) assay using a molecular beacon paired with HRPzyme. Anal Bioanal Chem 2023; 415:4973-4984. [PMID: 37365333 DOI: 10.1007/s00216-023-04803-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023]
Abstract
Contamination by Escherichia coli O157:H7 is considered a threat in the livestock and food industries. Therefore, it is necessary to develop methods for the convenient and rapid detection of Shiga-toxin-producing E. coli O157:H7. This study aimed to develop a colorimetric loop-mediated isothermal amplification (cLAMP) assay using a molecular beacon to rapidly detect E. coli O157:H7. Primers and a molecular beacon were designed for targeting the Shiga-toxin-producing virulence genes (stx1 and stx2) as molecular markers. Additionally, Bst polymerase concentration and amplification conditions for bacterial detection were optimized. The sensitivity and specificity of the assay were also investigated and validated on artificially tainted (100-104 CFU/g) Korean beef samples. The cLAMP assay could detect 1 × 101 CFU/g at 65 °C for both genes, and the assay was confirmed to be specific for E. coli O157:H7. The cLAMP takes about an hour and does not require expensive devices (e.g., thermal cycler and detector). Hence, the cLAMP assay proposed herein can be used in the meat industry as a fast and simple way to detect E. coli O157:H7.
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Affiliation(s)
- Jeong-Eun Lee
- Institute of Smart Farm Research Center, Gyeongsang National University, Gyeongnam, Jinju, 52828, Korea
| | | | - Hyun-Jin Park
- Division of Applied Life Science, Graduate School, Gyeongsang National University, Gyeongnam, Jinju, 52828, Korea
| | - Sol-A Kim
- Division of Applied Life Science, Graduate School, Gyeongsang National University, Gyeongnam, Jinju, 52828, Korea
| | - Won-Bo Shim
- Division of Applied Life Science, Graduate School, Gyeongsang National University, Gyeongnam, Jinju, 52828, Korea.
- Institute of Agricultural and Life Science, Gyeongsang National University, Gyeongnam, Jinju, 52828, Korea.
- Division of Food Science and Technology, Gyeongsang National University, Gyeongnam, Jinju, 52828, Korea.
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15
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Zhao Y, O'Keefe CM, Hsieh K, Cope L, Joyce SC, Pisanic TR, Herman JG, Wang TH. Multiplex Digital Methylation-Specific PCR for Noninvasive Screening of Lung Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206518. [PMID: 37039321 DOI: 10.1002/advs.202206518] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/18/2023] [Indexed: 06/04/2023]
Abstract
There remains tremendous interest in developing liquid biopsy assays for detection of cancer-specific alterations, such as mutations and DNA methylation, in cell-free DNA (cfDNA) obtained through noninvasive blood draws. However, liquid biopsy analysis is often challenging due to exceedingly low fractions of circulating tumor DNA (ctDNA), necessitating the use of extended tumor biomarker panels. While multiplexed PCR strategies provide advantages such as higher throughput, their implementation is often hindered by challenges such as primer-dimers and PCR competition. Alternatively, digital PCR (dPCR) approaches generally offer superior performance, but with constrained multiplexing capability. This paper describes development and validation of the first multiplex digital methylation-specific PCR (mdMSP) platform for simultaneous analysis of four methylation biomarkers for liquid-biopsy-based detection of non-small cell lung cancer (NSCLC). mdMSP employs a microfluidic device containing four independent, but identical modules, housing a total of 40 160 nanowells. Analytical validation of the mdMSP platform demonstrates multiplex detection at analytical specificities as low as 0.0005%. The clinical utility of mdMSP is also demonstrated in a cohort of 72 clinical samples of low-volume liquid biopsy specimens from patients with computed tomography (CT)-scan indeterminant pulmonary nodules, exhibiting superior clinical performance when compared to traditional MSP assays for noninvasive detection of early-stage NSCLC.
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Affiliation(s)
- Yang Zhao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Christine M O'Keefe
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Leslie Cope
- Department of Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Sonali C Joyce
- The UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Thomas R Pisanic
- Department of Oncology, Johns Hopkins University, Baltimore, MD, 21287, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - James G Herman
- The UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21287, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
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16
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Jia N, Wang C, Liu X, Huang X, Xiao F, Fu J, Sun C, Xu Z, Wang G, Zhou J, Wang Y. A CRISPR-Cas12a-based platform for ultrasensitive rapid highly specific detection of Mycobacterium tuberculosis in clinical application. Front Cell Infect Microbiol 2023; 13:1192134. [PMID: 37287467 PMCID: PMC10242030 DOI: 10.3389/fcimb.2023.1192134] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (MTB), is the second leading cause of death after COVID-19 pandemic. Here, we coupled multiple cross displacement amplification (MCDA) technique with CRISPR-Cas12a-based biosensing system to design a novel detection platform for tuberculosis diagnosis, termed MTB-MCDA-CRISPR. MTB-MCDA-CRISPR pre-amplified the specific sdaA gene of MTB by MCDA, and the MCDA results were then decoded by CRISPR-Cas12a-based detection, resulting in simple visual fluorescent signal readouts. A set of standard MCDA primers, an engineered CP1 primer, a quenched fluorescent ssDNA reporter, and a gRNA were designed targeting the sdaA gene of MTB. The optimal temperature for MCDA pre-amplification is 67°C. The whole experiment process can be completed within one hour, including sputum rapid genomic DNA extraction (15 minutes), MCDA reaction (40 minutes), and CRISPR-Cas12a-gRNA biosensing process (5 minutes). The limit of detection (LoD) of the MTB-MCDA-CRISPR assay is 40 fg per reaction. The MTB-MCDA-CRISPR assay does not cross reaction with non-tuberculosis mycobacterium (NTM) strains and other species, validating its specificity. The clinical performance of MTB-MCDA-CRISPR assay was higher than that of the sputum smear microscopy test and comparable to that of Xpert method. In summary, the MTB-MCDA-CRISPR assay is a promising and effective tool for tuberculosis infection diagnosis, surveillance and prevention, especially for point-of-care (POC) test and field deployment in source-limited regions.
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Affiliation(s)
- Nan Jia
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Chaohong Wang
- Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Xiaming Liu
- The Second Department of Geriatrics, Handan Central Hospital, Handan, Hebei, China
| | - Xiaolan Huang
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Fei Xiao
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Jin Fu
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Chunrong Sun
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Xu
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Guirong Wang
- Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Juan Zhou
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Yi Wang
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
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17
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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18
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de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
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Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
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19
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Biswas GC, Khan MTM, Das J. Wearable nucleic acid testing platform - A perspective on rapid self-diagnosis and surveillance of infectious diseases. Biosens Bioelectron 2023; 226:115115. [PMID: 36746023 DOI: 10.1016/j.bios.2023.115115] [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: 11/10/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Wearable biosensors (WB) are currently attracting considerable interest for rapid detection and monitoring of biomarkers including metabolites, protein, and pathogen in bodily fluids (e.g., sweat, saliva, tears, and interstitial fluid). Another branch of WB termed wearable nucleic acid testing (NAT) is blossoming thanks to the development of microfluidic technology and isothermal nucleic acid amplification technique (iNAAT); however, there are only few reports on this. The wearable NAT is an emerging field of point-of-care (POC) diagnostics, and holds the promise for time-saving self-diagnosis, and evidence-based surveillance of infectious diseases in remote or low-resource settings. The use of wearable NAT can also be advanced to include molecular diagnosis, the identification of cancer biomarkers, genetic abnormalities, and other aspects. The wearable NAT provides the potential for evidence-based surveillance of infectious diseases when combined with internet connectivity and App software. To make the wearable NAT accessible to the end users, however, improvements must be made to the fabrication, cost, speed, sensitivity, specificity, sampling, iNAAT, analyzer, and a few other features. So, in this paper, we looked at the wearable NAT's most recent development, identified its difficulties, and defined its potential for managing infectious diseases quickly in the future. This is the wearable NAT review's first effort. We expect that this article will provide the concise resources needed to develop and deploy an efficient wearable NAT system.
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Affiliation(s)
- Gokul Chandra Biswas
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
| | - Md Taufiqur Mannan Khan
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Jagotamoy Das
- Department of Chemistry, Northwestern University, 2170 Campus Dr, Evanston, IL, 60208, USA.
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20
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Gulinaizhaer A, Zou M, Ma S, Yao Y, Fan X, Wu G. Isothermal nucleic acid amplification technology in HIV detection. Analyst 2023; 148:1189-1208. [PMID: 36825492 DOI: 10.1039/d2an01813f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Nucleic acid testing for HIV plays an important role in the early diagnosis and monitoring of antiretroviral therapy outcomes in HIV patients and HIV-infected infants. Currently, the main molecular diagnostic methods employed are complex, time-consuming, and expensive to operate in resource-limited areas. Isothermal nucleic acid amplification technology overcomes some of the shortcomings of traditional assays and makes it possible to use point-of-care tests for molecular HIV detection. Here, we summarize and discuss the latest technological advances in isothermal nucleic acid amplification for HIV detection, with the intent of providing guidance for the development of subsequent HIV assays with high sensitivity and specificity.
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Affiliation(s)
- Abudushalamu Gulinaizhaer
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Mingyuan Zou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Shuo Ma
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Yuming Yao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Xiaobo Fan
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China.,Department of Laboratory Medicine, Medical School of Southeast University, Nanjing 210009, Jiangsu, China. .,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, Jiangsu, China
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21
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Krishnan SR, Soares RRG, Madaboosi N, Gromiha MM. AutoPLP: A Padlock Probe Design Pipeline for Zoonotic Pathogens. ACS Infect Dis 2023; 9:459-469. [PMID: 36790094 DOI: 10.1021/acsinfecdis.2c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Emergence of novel zoonotic infections among the human population has increased the burden on global healthcare systems to curb their spread. To meet the evolutionary agility of pathogens, it is essential to revamp the existing diagnostic methods for early detection and characterization of the pathogens at the molecular level. Padlock probes (PLPs), which can leverage the power of isothermal nucleic acid amplification techniques (NAAT) such as rolling circle amplification (RCA), are known for their high sensitivity and specificity in detecting a diverse pathogen panel of interest. However, due to the complexity involved in deciding the target regions for PLP design and the need for optimization of multiple experimental parameters, the applicability of RCA has been limited in point-of-care testing for pathogen detection. To address this gap, we have developed a novel and integrated PLP design pipeline named AutoPLP, which can automate the probe design process for a diverse pathogen panel of interest. The pipeline is composed of three modules which can perform sequence data curation, multiple sequence alignment, conservation analysis, filtration based on experimental parameters (Tm, GC content, and secondary structure formation), and in silico probe validation via potential cross-hybridization check with host genome. The modules can also take into account the backbone and restriction site information, appropriate combinations of which are incorporated along with the probe arms to design a complete probe sequence. The potential applications of AutoPLP are showcased through the design of PLPs for the detection of rabies virus and drug-resistant strains of Mycobacterium tuberculosis.
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Affiliation(s)
- Sowmya Ramaswamy Krishnan
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.,TCS Research (Life Sciences Division), Tata Consultancy Services, Hyderabad 500081, India
| | - Ruben R G Soares
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna SE-17121, Sweden
| | - Narayanan Madaboosi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.,International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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22
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Song M, Hong S, Lee LP. Multiplexed Ultrasensitive Sample-to-Answer RT-LAMP Chip for the Identification of SARS-CoV-2 and Influenza Viruses. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207138. [PMID: 36398425 DOI: 10.1002/adma.202207138] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Prompt on-site diagnosis of SARS-CoV-2 with other respiratory infections will have minimized the global impact of the COVID-19 pandemic through rapid, effective management. However, no such multiplex point-of-care (POC) chip has satisfied a suitable sensitivity of gold-standard nucleic acid amplification tests (NAATs). Here, a rapid multiplexed ultrasensitive sample-to-answer loop-mediated isothermal amplification (MUSAL) chip operated by simple LED-driven photothermal amplification to detect six targets from single-swab sampling is presented. First, the MUSAL chip allows ultrafast on-chip sample preparation with ≈500-fold preconcentration at a rate of 1.2 mL min-1 . Second, the chip enables contamination-free amplification using autonomous target elution into on-chip reagents by photothermal activation. Finally, the chip accomplishes multiplexed on-chip diagnostics of SARS-CoV-2 and influenza viruses with a limit of detection (LoD) of 0.5 copies µL-1 . The rapid, ultrasensitive, cost-effective sample-to-answer chip with a multiplex capability will allow timely management of various pandemics situations that may be faced shortly.
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Affiliation(s)
- Minsun Song
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - SoonGweon Hong
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, Gyeonggi-do, 16419, Republic of Korea
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23
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Fei Z, Liu P, Cheng C, Wei R, Xiao P, Zhang Y. Solvent-Responsive Magnetic Beads for Accurate Detection of SARS-CoV-2. ACS APPLIED MATERIALS & INTERFACES 2023; 15:4924-4934. [PMID: 36648175 DOI: 10.1021/acsami.2c18684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Although numerous approaches were proposed for the nucleic acid (NA)-based SARS-CoV-2 detection, the nonideal NA desorption efficiency of conventional magnetic beads (MBs) limits their widespread application. In this study, we developed solvent-responsive MBs (called responsive MBs), which, in the presence of buffers, modulated the absorption and desorption capacities of NA by flipping the surface -COO-. Relative to other commercial MBs, responsive MBs exhibited similar absorption profiles and markedly enhanced desorption profiles. When applied for NA detection of complex samples, responsive MBs exhibited better performance of RNA detection than DNA, with obvious advantages in sensitivity. Specifically, the RNA and DNA desorption rates of commercial MBs were ∼85 and 82.5%, while those of responsive MBs were nearly 94 and 93.5%, respectively. Furthermore, responsive MBs exhibited remarkable extraction ability in a wide range of tissues and better performance of RNA extraction than DNA. When applied for SARS-CoV-2 detection, the responsive MBs along with the simulated digital RT-LAMP (a previously established apparatus) further improved detection efficiency, yielding a precise quantitative detection as low as 25 copies and an ultimate sensibility detection of 5 copies/mL. It was also successfully employed in numerous NA-based technologies such as polymerase chain reaction (PCR), sequencing, and so on.
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Affiliation(s)
- Zhongjie Fei
- Jiangsu Key Laboratory of Advanced Metallic Materials, School of Materials Science and Engineering, Southeast University, No. 2, Southeast University Road, Nanjing 211189, Jiangsu, China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Xuanwu Road, Nanjing 210096, Jiangsu, China
| | - Ping Liu
- Jiangsu Key Laboratory of Advanced Metallic Materials, School of Materials Science and Engineering, Southeast University, No. 2, Southeast University Road, Nanjing 211189, Jiangsu, China
| | - Chu Cheng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Xuanwu Road, Nanjing 210096, Jiangsu, China
| | - Rongbin Wei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Xuanwu Road, Nanjing 210096, Jiangsu, China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Xuanwu Road, Nanjing 210096, Jiangsu, China
| | - Youfa Zhang
- Jiangsu Key Laboratory of Advanced Metallic Materials, School of Materials Science and Engineering, Southeast University, No. 2, Southeast University Road, Nanjing 211189, Jiangsu, China
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24
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He H, Zhou Y, Chen B, Zhang Y, Zhong X, Xu L, Guo B, Yin C, Zhou X, Li Q, Huang Z, Luo G, Guo X. Nucleic acid amplification with specific signal filtration and magnification for ultrasensitive colorimetric detection. Talanta 2023; 253:123978. [PMID: 36209643 DOI: 10.1016/j.talanta.2022.123978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]
Abstract
Recently, sensitive, fast and low cost nucleic acid isothermal amplification technologies (such as loop-mediated isothermal amplification, LAMP) have attracted great attention in the urgent needs of point-of-care testing (POCT) and regular epidemic prevention and control. However, unlike PCR which usually employs TaqMan probe to report specific signals, specific-signal-output strategies in isothermal amplification are immature and visual detection even rare, which limits their popularity in POCT. We hypothesize to address this issue by designing a visual-signal-report system to both filtrate and magnify the target information in isothermal amplification. In this work, we developed a specific signal filtration and magnification colorimetric isothermal sensing platform (SFMC for short) for ultrasensitive detection of DNA and RNA. SFMC consists of two processes: an isothermal amplification with specific signal filtration and a self-replication catalyzed hairpin assembly (SRCHA) for rapid target-specific signal magnification and outputting. With these unique properties, this biosensing platform could detect target DNA as low as 5 copies per reaction and target RNA as low as 10 copies per reaction by naked eyes. Benefited from the excellent colorimetric detection performance, this biosensing platform has been successfully used for African swine fever virus (ASFV) and SARS-CoV-2 detection.
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Affiliation(s)
- Hongfei He
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Yan Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China; School of Pharmacy & School of Preclinical Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Chen
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Yi Zhang
- Sichuan Provincial Center for Animal Disease Control and Prevention, Chengdu, 610041, PR China
| | - Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Lei Xu
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Bin Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Chong Yin
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xi Zhou
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Qingrong Li
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, PR China.
| | - Guangcheng Luo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Translational Medicine Research Center & Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, PR China.
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25
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Wang J, Jiang H, Pan L, Gu X, Xiao C, Liu P, Tang Y, Fang J, Li X, Lu C. Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems. Front Bioeng Biotechnol 2023; 11:1020430. [PMID: 36815884 PMCID: PMC9930993 DOI: 10.3389/fbioe.2023.1020430] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
As nucleic acid testing is playing a vital role in increasingly many research fields, the need for rapid on-site testing methods is also increasing. The test procedure often consists of three steps: Sample preparation, amplification, and detection. This review covers recent advances in on-chip methods for each of these three steps and explains the principles underlying related methods. The sample preparation process is further divided into cell lysis and nucleic acid purification, and methods for the integration of these two steps on a single chip are discussed. Under amplification, on-chip studies based on PCR and isothermal amplification are covered. Three isothermal amplification methods reported to have good resistance to PCR inhibitors are selected for discussion due to their potential for use in direct amplification. Chip designs and novel strategies employed to achieve rapid extraction/amplification with satisfactory efficiency are discussed. Four detection methods providing rapid responses (fluorescent, optical, and electrochemical detection methods, plus lateral flow assay) are evaluated for their potential in rapid on-site detection. In the final section, we discuss strategies to improve the speed of the entire procedure and to integrate all three steps onto a single chip; we also comment on recent advances, and on obstacles to reducing the cost of chip manufacture and achieving mass production. We conclude that future trends will focus on effective nucleic acid extraction via combined methods and direct amplification via isothermal methods.
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Affiliation(s)
- Jingwen Wang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Han Jiang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Leiming Pan
- Zhejiang Hongzheng Testing Co., Ltd., Ningbo, China
| | - Xiuying Gu
- Zhejiang Gongzheng Testing Center Co., Ltd., Hangzhou, China
| | - Chaogeng Xiao
- Institute of Food Science, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Pengpeng Liu
- Key Laboratory of Biosafety detection for Zhejiang Market Regulation, Zhejiang Fangyuan Testing Group LO.T, Hangzhou, China
| | - Yulong Tang
- Hangzhou Tiannie Technology Co., Ltd., Hangzhou, China
| | - Jiehong Fang
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiaoqian Li
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Chenze Lu
- Key Laboratory of Specialty Agri-products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
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26
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COVID-19 diagnostic approaches with an extensive focus on computed tomography in accurate diagnosis, prognosis, staging, and follow-up. Pol J Radiol 2023; 88:e53-e64. [PMID: 36819223 PMCID: PMC9907165 DOI: 10.5114/pjr.2023.124597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/12/2022] [Indexed: 02/10/2023] Open
Abstract
Although a long time has passed since its outbreak, there is currently no specific treatment for COVID-19, and it seems that the most appropriate strategy to combat this pandemic is to identify and isolate infected individuals. Various clinical diagnosis methods such as molecular techniques, serologic assays, and imaging techniques have been developed to identify suspected patients. Although reverse transcription-quantitative PCR (RT-qPCR) has emerged as a reference standard method for diagnosis of SARS-CoV-2, the high rate of false-negative results and limited supplies to meet current demand are the main shortcoming of this technique. Based on a comprehensive literature review, imaging techniques, particularly computed tomography (CT), show an acceptable level of sensitivity in the diagnosis and follow-up of COVID-19. Indeed, because lung infection or pneumonia is a common complication of COVID-19, the chest CT scan can be an alternative testing method in the early diagnosis and treatment assessment of the disease. In this review, we summarize all the currently available frontline diagnostic tools for the detection of SARS-CoV-2-infected individuals and highlight the value of chest CT scan in the diagnosis, prognosis, staging, management, and follow-up of infected patients.
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27
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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28
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Dangerfield TL, Paik I, Bhadra S, Johnson KA, Ellington A. Kinetics of elementary steps in loop-mediated isothermal amplification (LAMP) show that strand invasion during initiation is rate-limiting. Nucleic Acids Res 2023; 51:488-499. [PMID: 36583345 PMCID: PMC9841402 DOI: 10.1093/nar/gkac1221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has proven to be easier to implement than PCR for point-of-care diagnostic tests. However, the underlying mechanism of LAMP is complicated and the kinetics of the major steps in LAMP have not been fully elucidated, which prevents rational improvements in assay development. Here we present our work to characterize the kinetics of the elementary steps in LAMP and show that: (i) strand invasion / initiation is the rate-limiting step in the LAMP reaction; (ii) the loop primer plays an important role in accelerating the rate of initiation and does not function solely during the exponential amplification phase and (iii) strand displacement synthesis by Bst-LF polymerase is relatively fast (125 nt/s) and processive on both linear and hairpin templates, although with some interruptions on high GC content templates. Building on these data, we were able to develop a kinetic model that relates the individual kinetic experiments to the bulk LAMP reaction. The assays developed here provide important insights into the mechanism of LAMP, and the overall model should be crucial in engineering more sensitive and faster LAMP reactions. The kinetic methods we employ should likely prove useful with other isothermal DNA amplification methods.
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Inyup Paik
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Sanchita Bhadra
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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29
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Rubio-Monterde A, Quesada-González D, Merkoçi A. Toward Integrated Molecular Lateral Flow Diagnostic Tests Using Advanced Micro- and Nanotechnology. Anal Chem 2023; 95:468-489. [PMID: 36413136 DOI: 10.1021/acs.analchem.2c04529] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Ana Rubio-Monterde
- Paperdrop Diagnostics S.L., MRB, Campus UAB, 08193 Bellaterra, Spain.,Nanobioelectronics and Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, 08193 Barcelona, Spain
| | | | - Arben Merkoçi
- Paperdrop Diagnostics S.L., MRB, Campus UAB, 08193 Bellaterra, Spain.,Nanobioelectronics and Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, 08193 Barcelona, Spain.,The Barcelona Institute of Science and Technology (BIST), Campus UAB, 08036 Bellaterra, Barcelona Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Pg. Lluis Companys 23, 08010 Barcelona, Spain
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30
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Li Y, Kim H, Ju Y, Park Y, Kang T, Yong D, Park HG. Ultrasensitive Isothermal Detection of SARS-CoV-2 Based on Self-Priming Hairpin-Utilized Amplification of the G-Rich Sequence. Anal Chem 2022; 94:17448-17455. [PMID: 36480911 PMCID: PMC9743493 DOI: 10.1021/acs.analchem.2c03442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
The outbreak of the novel coronavirus disease 2019 (COVID-19) pandemic induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of fatalities all over the world. Unquestionably, the effective and timely testing for infected individuals is the most imperative for the prevention of the ongoing pandemic. Herein, a new method was established for detecting SARS-CoV-2 based on the self-priming hairpin-utilized isothermal amplification of the G-rich sequence (SHIAG). In this strategy, the target RNA binding to the hairpin probe (HP) was uniquely devised to lead to the self-priming-mediated extension followed by the continuously repeated nicking and extension reactions, consequently generating abundant G-rich sequences from the intended reaction capable of producing fluorescence signals upon specifically interacting with thioflavin T (ThT). Based on the unique isothermal design concept, we successfully identified SARS-CoV-2 genomic RNA (gRNA) as low as 0.19 fM with excellent selectivity by applying only a single HP and further verified its practical diagnostic capability by reliably testing a total of 100 clinical specimens for COVID-19 with 100% clinical sensitivity and specificity. This study would provide notable insights into the design and evolution of new isothermal strategies for the sensitive and facile detection of SARS-CoV-2 under resource constraints.
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Affiliation(s)
- Yan Li
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Hansol Kim
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Yong Ju
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Yeonkyung Park
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea
Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu,
Daejeon34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan
University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do16419,
Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and
Research Institute of Bacterial Resistance, Yonsei University College of
Medicine, Seoul03722, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
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31
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Pang L, Pi X, Yang X, Song D, Qin X, Wang L, Man C, Zhang Y, Jiang Y. Nucleic acid amplification-based strategy to detect foodborne pathogens in milk: a review. Crit Rev Food Sci Nutr 2022; 64:5398-5413. [PMID: 36476145 DOI: 10.1080/10408398.2022.2154073] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Milk contaminated with trace amounts of foodborne pathogens can considerably threaten food safety and public health. Therefore, rapid and accurate detection techniques for foodborne pathogens in milk are essential. Nucleic acid amplification (NAA)-based strategies are widely used to detect foodborne pathogens in milk. This review article covers the mechanisms of the NAA-based detection of foodborne pathogens in milk, including polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), rolling circle amplification (RCA), and enzyme-free amplification, among others. Key factors affecting detection efficiency and the advantages and disadvantages of the above techniques are analyzed. Potential on-site detection tools based on NAA are outlined. We found that NAA-based strategies were effective in detecting foodborne pathogens in milk. Among them, PCR was the most reliable. LAMP showed high specificity, whereas RPA and RCA were most suitable for on-site and in-situ detection, respectively, and enzyme-free amplification was more economical. However, factors such as sample separation, nucleic acid target conversion, and signal transduction affected efficiency of NAA-based strategies. The lack of simple and effective sample separation methods to reduce the effect of milk matrices on detection efficiency was noteworthy. Further research should focus on simplifying, integrating, and miniaturizing microfluidic on-site detection platforms.
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Affiliation(s)
- Lidong Pang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xiaowen Pi
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Danliangmin Song
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xue Qin
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Lihan Wang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yu Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
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Tetz G, Tetz V. Overcoming Antibiotic Resistance with Novel Paradigms of Antibiotic Selection. Microorganisms 2022; 10:2383. [PMID: 36557636 PMCID: PMC9781420 DOI: 10.3390/microorganisms10122383] [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: 11/05/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Conventional antimicrobial susceptibility tests, including phenotypic and genotypic methods, are insufficiently accurate and frequently fail to identify effective antibiotics. These methods predominantly select therapies based on the antibiotic response of only the lead bacterial pathogen within pure bacterial culture. However, this neglects the fact that, in the majority of human infections, the lead bacterial pathogens are present as a part of multispecies communities that modulate the response of these lead pathogens to antibiotics and that multiple pathogens can contribute to the infection simultaneously. This discrepancy is a major cause of the failure of antimicrobial susceptibility tests to detect antibiotics that are effective in vivo. This review article provides a comprehensive overview of the factors that are missed by conventional antimicrobial susceptibility tests and it explains how accounting for these methods can aid the development of novel diagnostic approaches.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, New York, NY 100141, USA
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33
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Rapid detection of φX-174 virus based on synchronous fluorescence of tryptophan. Anal Bioanal Chem 2022; 415:509-515. [PMID: 36441232 PMCID: PMC9702944 DOI: 10.1007/s00216-022-04436-2] [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: 09/06/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022]
Abstract
The development of rapid methods for the detection of virus particles based on their intrinsic fluorescence (the native auto-fluorescence that originates from the non-labeled analyte) is challenging. Pure viruses may be detected in filtered solutions, based on the strong fluorescence of the amino acid tryptophan (Trp) in their proteins. Nevertheless, Trp also exists in high quantities in the hosts and host cultivation media. In this work, we developed a new method for the detection of the naked φX-174 virus. We show that a separation of φX-174 from its Escherichia coli host (grown on the standard cultivation medium nutrient agar) by simple extraction and filtration is not sufficient for its detection based on the intrinsic fluorescence since ~ 70% of the Trp fluorescence is derived from impurities. We formulate a new cultivation medium with a very low Trp concentration. We apply synchronous fluorescence measurements to show that no Trp fluorescence is detected in the extract solution upon incubation of this medium substrate with ammonium acetate extraction buffer. Finally, we apply synchronous fluorescence to detect φX-174 based on the spectral fingerprint of its native Trp content. Such a method is more rapid than usual traditional separation and detection methods which can take several hours and does not require any addition of labeling agents such as fluorescent dyes or antibodies for the detection. As other virus species contain Trp as one of the amino acids presents in their proteins, this method has the potential to apply to the detection of other viral species.
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Lin H, Zheng W, Li S, Wang Y, Wei D, Xie L, Lu W, Tian Z, Wang S, Qu J, Liu J. Internet of medical things-enabled CRISPR diagnostics for rapid detection of SARS-CoV-2 variants of concern. Front Microbiol 2022; 13:1070940. [PMID: 36466682 PMCID: PMC9715597 DOI: 10.3389/fmicb.2022.1070940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 10/31/2022] [Indexed: 02/12/2024] Open
Abstract
Previous studies have highlighted CRISPR-based nucleic acid detection as rapid and sensitive diagnostic methods for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we reported an optimized CRISPR-Cas12a diagnostic platform for the safe and rapid detection of SARS-CoV-2 variants of concern (VOCs). This platform, which was referred to as CALIBURN-v2, could complete the diagnosis on extracted RNA samples within 25 min in a closed-lid reaction mode and had 100-fold increase in detection sensitivity in comparison with previous platforms. Most importantly, by integrating a portable device and smartphone user interface, CALIBURN-v2 allowed for cloud server-based data collection and management, thus transforming the point-of-care testing (POCT) platform to internet of medical things (IoMT) applications. It was found that IoMT-enabled CALIBURN-v2 could achieve 95.56% (172 out of 180) sensitivity for SARS-CoV-2 wild type and 94.38% (84 out of 89) overall sensitivity for SARS-CoV-2 variants including Delta and Omicron strains. Therefore, our study provides a feasible approach for IoMT-enabled CRISPR diagnostics for the detection of SARS-CoV-2 VOCs.
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Affiliation(s)
- Huihuang Lin
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Weibo Zheng
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Yu Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Dong Wei
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leiying Xie
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Lu
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Shaowei Wang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
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McCloskey D, Boza J, Mason CE, Erickson D. MINI: A high-throughput point-of-care device for performing hundreds of nucleic acid tests per day. Biosens Bioelectron 2022; 216:114654. [PMID: 36084523 PMCID: PMC10960951 DOI: 10.1016/j.bios.2022.114654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/11/2022] [Accepted: 08/20/2022] [Indexed: 11/24/2022]
Abstract
There are a variety of infectious diseases with a high incidence and mortality in limited resource settings that could benefit from rapid point of care molecular diagnosis. Global health efforts have sought to implement mass-screening programs to provide earlier detection and subsequent treatment in an effort to control transmission and improve health outcomes. However, many of the current diagnostic technologies under development are limited to fewer than 10 samples per run, which inherently restricts the screening throughput of these devices. We have developed a high throughput device called "MINI" that is capable of testing hundreds of samples per day at the point-of-care. MINI can utilize multiple energy sources - electricity, flame, or solar - to perform loop-mediated isothermal amplification (LAMP) in a portable and robust device which is ideal for use in limited resource settings. The unique opto-electronic design of MINI minimizes the energy and space requirements of the device and maximizes the optical isolation and signal clarity, enabling point-of-care analysis of 96 unique samples at once. We show comparable performance to a commercial instrument using two different LAMP assays for Kaposi's sarcoma-associated herpesvirus and a common housekeeping gene, GAPDH. With a single device capable of running hundreds of samples per day, increased access to modern molecular diagnostics could improve health outcomes for a variety of diseases common in limited resource settings.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Juan Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Christopher E Mason
- Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - David Erickson
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA; Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
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Schmitz JE, Stratton CW, Persing DH, Tang YW. Forty Years of Molecular Diagnostics for Infectious Diseases. J Clin Microbiol 2022; 60:e0244621. [PMID: 35852340 PMCID: PMC9580468 DOI: 10.1128/jcm.02446-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.
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Affiliation(s)
- Jonathan E. Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David H. Persing
- Medical and Scientific Affairs, Cepheid, Sunnyvale, California, USA
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
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37
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Liu KS, Mao XD, Ni W, Li TP. Laboratory detection of SARS-CoV-2: A review of the current literature and future perspectives. Heliyon 2022; 8:e10858. [PMID: 36212015 PMCID: PMC9527186 DOI: 10.1016/j.heliyon.2022.e10858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/16/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Nowadays, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), whose infectivity is awfully strong, has been a major global threat to the public health. Since lung is the major target of SARS-CoV-2, the infection can lead to respiratory distress syndrome (RDS), multiple organ failure (MOF), and even death. The studies on viral structure and infection mechanism have found that angiotensin-converting enzyme 2 (ACE2), a pivotal enzyme affecting the organ-targeting in the RAS system, is the receptor of the SARS-CoV-2 virus. Currently, the detection of SARSCoV-2 is mainly achieved using open plate real-time reverse-transcription polymerase chain reaction (RT-PCR). While open plate method has some limitations, such as a high false-negative rate, cumbersome manual operation, aerosol pollution and leakage risks. Therefore, a convenient method to rapidly detect SARS-CoV-2 virus is urgently and extremely required for timely epidemic control with the limited resources. In this review, the current real-time methods and principles for novel coronavirus detection are summarized, with the aim to provide a reference for real-time screening of coronavirus in areas with insufficient detection capacity and inadequate medical resources. The development and establishment of a rapid, simple, sensitive and specific system to detect SARS-CoV-2 is of vital importance for distinct diagnosis and effective treatment of the virus, especially in the flu season.
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Affiliation(s)
- Kang-Sheng Liu
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210029, China
| | - Xiao-Dong Mao
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China,Key Laboratory of TCM Syndrome & Treatment of Yingbing of State Administration of Traditional Chinese Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing 210028, China
| | - Wenjing Ni
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China,Key Laboratory of TCM Syndrome & Treatment of Yingbing of State Administration of Traditional Chinese Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing 210028, China
| | - Tai-Ping Li
- Department of Neuro-Psychiatric Institute, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing 210029, China,Corresponding author.
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38
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Toldrà A, Ainla A, Khaliliazar S, Landin R, Chondrogiannis G, Hanze M, Réu P, Hamedi MM. Portable electroanalytical nucleic acid amplification tests using printed circuit boards and open-source electronics. Analyst 2022; 147:4249-4256. [PMID: 35993403 PMCID: PMC9511072 DOI: 10.1039/d2an00923d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/10/2022] [Indexed: 09/19/2023]
Abstract
The realization of electrochemical nucleic acid amplification tests (NAATs) at the point of care (POC) is highly desirable, but it remains a challenge given their high cost and lack of true portability/miniaturization. Here we show that mass-produced, industrial standardized, printed circuit boards (PCBs) can be repurposed to act as near-zero cost electrodes for self-assembled monolayer-based DNA biosensing, and further integration with a custom-designed and low-cost portable potentiostat. To show the analytical capability of this system, we developed a NAAT using isothermal recombinase polymerase amplification, bypassing the need of thermal cyclers, followed by an electrochemical readout relying on a sandwich hybridization assay. We used our sensor and device for analytical detection of the toxic microalgae Ostreopsis cf. ovata as a proof of concept. This work shows the potential of PCBs and open-source electronics to be used as powerful POC DNA biosensors at a low-cost.
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Affiliation(s)
- Anna Toldrà
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Alar Ainla
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Shirin Khaliliazar
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Roman Landin
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Georgios Chondrogiannis
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Martin Hanze
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Pedro Réu
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
| | - Mahiar M Hamedi
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, KTH Royal Institute of Technology, Stockholm 10044, Sweden.
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Kline EC, Panpradist N, Hull IT, Wang Q, Oreskovic AK, Han PD, Starita LM, Lutz BR. Multiplex Target-Redundant RT-LAMP for Robust Detection of SARS-CoV-2 Using Fluorescent Universal Displacement Probes. Microbiol Spectr 2022; 10:e0158321. [PMID: 35708340 PMCID: PMC9430505 DOI: 10.1128/spectrum.01583-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/06/2022] [Indexed: 11/20/2022] Open
Abstract
The increasing prevalence of variant lineages during the COVID-19 pandemic has the potential to disrupt molecular diagnostics due to mismatches between primers and variant templates. Point-of-care molecular diagnostics, which often lack the complete functionality of their high-throughput laboratory counterparts, are particularly susceptible to this type of disruption, which can result in false-negative results. To address this challenge, we have developed a robust Loop Mediated Isothermal Amplification assay with single tube multiplexed multitarget redundancy and an internal amplification control. A convenient and cost-effective target-specific fluorescence detection system allows amplifications to be grouped by signal using adaptable probes for pooled reporting of SARS-CoV-2 target amplifications or differentiation of the Internal Amplification Control. Over the course of the pandemic, primer coverage of viral lineages by the three redundant sub-assays has varied from assay to assay as they have diverged from the Wuhan-Hu-1 isolate sequence, but aggregate coverage has remained high for all variant sequences analyzed, with a minimum of 97.4% (Variant of Interest: Eta). In three instances (Delta, Gamma, Eta), a high-frequency mismatch with one of the three sub-assays was observed, but overall coverage remained high due to multitarget redundancy. When challenged with extracted human samples the multiplex assay showed 87% or better sensitivity (of 30 positive samples), with 100% sensitivity for samples containing greater than 30 copies of viral RNA per reaction (of 21 positive samples), and 100% specificity (of 60 negative samples). These results are further evidence that conventional laboratory methodologies can be leveraged at the point of care for robust performance and diagnostic stability over time. IMPORTANCE The COVID-19 pandemic has had tremendous impact, and the ability to perform molecular diagnostics in resource limited settings has emerged as a key resource for mitigating spread of the disease. One challenge in COVID-19 diagnosis, as well as other viruses, is ongoing mutation that can allow viruses to evade detection by diagnostic tests. We developed a test that detects multiple parts of the virus genome in a single test to reduce the chance of missing a virus due to mutation, and it is designed to be simpler and faster than typical laboratory tests while maintaining high sensitivity. This capability is enabled by a novel fluorescent probe technology that works with a simple constant temperature reaction condition.
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Affiliation(s)
- Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health for Women Adolescents and Children, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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Liu S, Zhao K, Huang M, Zeng M, Deng Y, Li S, Chen H, Li W, Chen Z. Research progress on detection techniques for point-of-care testing of foodborne pathogens. Front Bioeng Biotechnol 2022; 10:958134. [PMID: 36003541 PMCID: PMC9393618 DOI: 10.3389/fbioe.2022.958134] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/30/2022] [Indexed: 11/21/2022] Open
Abstract
The global burden of foodborne disease is enormous and foodborne pathogens are the leading cause of human illnesses. The detection of foodborne pathogenic bacteria has become a research hotspot in recent years. Rapid detection methods based on immunoassay, molecular biology, microfluidic chip, metabolism, biosensor, and mass spectrometry have developed rapidly and become the main methods for the detection of foodborne pathogens. This study reviewed a variety of rapid detection methods in recent years. The research advances are introduced based on the above technical methods for the rapid detection of foodborne pathogenic bacteria. The study also discusses the limitations of existing methods and their advantages and future development direction, to form an overall understanding of the detection methods, and for point-of-care testing (POCT) applications to accurately and rapidly diagnose and control diseases.
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Affiliation(s)
- Sha Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Kaixuan Zhao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Meiyuan Huang
- Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Department of Pathology, Central South University, Zhuzhou, China
| | - Meimei Zeng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Wen Li
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
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41
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Chen X, Yuan W, Zhou Q, Tan Y, Wang R, Dong S. Sensitive and visual identification of Chlamydia trachomatis using multiple cross displacement amplification integrated with a gold nanoparticle-based lateral flow biosensor for point-of-care use. Front Cell Infect Microbiol 2022; 12:949514. [PMID: 35937700 PMCID: PMC9355032 DOI: 10.3389/fcimb.2022.949514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infection (STI) and remains a major public health challenge, especially in less-developed regions. Establishing a rapid, inexpensive, and easy-to-interpret point-of-care (POC) testing system for C. trachomatis could be critical for its treatment and limiting further transmission. Here, we devised a novel approach termed a multiple cross displacement amplification integrated with gold nanoparticle-based lateral flow biosensor (MCDA-AuNPs-LFB) for the highly specific, sensitive, user-friendly, and rapid identification of C. trachomatis in clinical samples. A suite of MCDA primers based on the C. trachomatis ompA gene from 14 serological variants (serovar A-K, L1, L2, and L3) were successfully designed and used to establish the assay. Optimal assay conditions were identified at 67°C, and the detection procedure, including nucleic acid preparation (approximately 5 min), MCDA amplification (30 min), and AuNPs-LFB visual readout (within 2 min), was completed within 40 min. The all-in cost for each test was approximately $5.5 USD. The limit of detection (LoD) was 10 copies/reaction, and no cross-reaction was observed with non-C. trachomatis microbes. A total of 135 suspected C. trachomatis-infection genital secretion samples were collected and simultaneously detected using real-time quantitative PCR (qPCR) in our assay. Compared with the qPCR technology, the MCDA-AuNPs-LFB sensitivity, specificity, positive predictive value, and negative predictive value were 100%, 96.20%, 94.92%, and 100%, respectively. Hence, our MCDA-AuNP-LFB assay exhibited considerable potential for POC testing and could be used to identify C. trachomatis in clinical settings, particularly in low-income regions.
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Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- Clinical Medical Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wei Yuan
- Quality Control Department, Guizhou Provincial Center for Clinical Laboratory, Guiyang, China
| | - Qingxue Zhou
- Clinical Laboratory, Hangzhou Women’s Hospital, Hangzhou, China
| | - Yan Tan
- Quality Control Department, Guizhou Provincial Center for Clinical Laboratory, Guiyang, China
| | - Ronghua Wang
- Department of Clinical Laboratory, Longli people’s Hospital, Qianlan, China
| | - Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
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Gerace E, Mancuso G, Midiri A, Poidomani S, Zummo S, Biondo C. Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections. Pathogens 2022; 11:pathogens11060663. [PMID: 35745518 PMCID: PMC9229729 DOI: 10.3390/pathogens11060663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.
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Affiliation(s)
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Stefano Poidomani
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
- Correspondence: ; Tel.: +39-090-2213322
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Wu H, Zou M, Fan X, Su F, Xiao F, Zhou M, Sun Y, Zhao F, Wu G. Facile, Rapid, and Low-Cost Detection for Influenza Viruses and Respiratory Syncytial Virus Based on a Catalytic DNA Assembly Circuit. ACS OMEGA 2022; 7:15074-15081. [PMID: 35557683 PMCID: PMC9089383 DOI: 10.1021/acsomega.2c00882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/30/2022] [Indexed: 05/13/2023]
Abstract
Influenza viruses and respiratory syncytial virus (RSV) have contributed to severe respiratory infections, causing huge economic and healthcare burdens. To achieve rapid and precise detection of influenza viruses and RSV, we proposed a catalytic hairpin assembly (CHA) combined with the lateral flow immunoassay (CHA-LFIA) detection method. The presence of the target RNA triggers the initiation of CHA circuits. H1/H2 complexes, the amplified signal products, which were labeled with digoxin and biotin, were detected with a highly sensitive lateral flow immunoassay system. The sensitivity of the CHA-LFIA system to influenza A and B viruses and RSV reached up to 1, 1, and 5 pM, respectively. In addition, this method exhibited excellent capability for differentiating between target RNA and base-mismatched RNA. The results demonstrated that an enzyme-free, rapid, highly sensitive, and specific method had been developed to detect influenza A and B viruses and RSV.
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Affiliation(s)
- Huina Wu
- Medical
School of Southeast University, Nanjing 210009, People’s
Republic of China
| | - Mingyuan Zou
- Medical
School of Southeast University, Nanjing 210009, People’s
Republic of China
| | - Xiaobo Fan
- Medical
School of Southeast University, Nanjing 210009, People’s
Republic of China
| | - Feiya Su
- Medical
School of Southeast University, Nanjing 210009, People’s
Republic of China
| | - Feng Xiao
- Medical
School of Southeast University, Nanjing 210009, People’s
Republic of China
| | - Meiling Zhou
- Medical
School of Southeast University, Nanjing 210009, People’s
Republic of China
| | - Yan Sun
- Medical
School of Southeast University, Nanjing 210009, People’s
Republic of China
| | - Fengfeng Zhao
- Medical
School of Southeast University, Nanjing 210009, People’s
Republic of China
| | - Guoqiu Wu
- Center
of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, People’s Republic
of China
- Diagnostics
Department, Medical School of Southeast
University, Nanjing 210009, People’s Republic of China
- Jiangsu
Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing 210009, People’s Republic
of China
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Cao S, Tang X, Chen T, Chen G. Types and Applications of Nicking Enzyme-Combined Isothermal Amplification. Int J Mol Sci 2022; 23:ijms23094620. [PMID: 35563012 PMCID: PMC9100243 DOI: 10.3390/ijms23094620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/03/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
Due to the sudden outbreak of COVID-19 at the end of 2019, rapid detection has become an urgent need for community clinics and hospitals. The rapid development of isothermal amplification detection technology for nucleic acids in the field of molecular diagnostic point-of-care testing (POCT) has gained a great deal of attention in recent years. Thanks to intensive research on nicking enzymes, nicking enzyme-combined isothermal amplification has become a promising platform for rapid detection. This is a novel technique that uses nicking enzymes to improve ordinary isothermal amplification. It has garnered significant interest as it overcomes the complexity of traditional molecular diagnostics and is not subject to temperature limitations, relying on cleavage enzymes to efficiently amplify targets in a very short time to provide a high level of amplification efficiency. In recent years, several types of nicking enzyme-combined isothermal amplification have been developed and they have shown great potential in molecular diagnosis, immunodiagnosis, biochemical identification, and other fields. However, this kind of amplification has some disadvantages. In this review, the principles, advantages and disadvantages, and applications of several nicking enzyme-combined isothermal amplification techniques are reviewed and the prospects for the development of these techniques are also considered.
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Affiliation(s)
- Siyu Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
| | - Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children’s Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
- Correspondence: (T.C.); (G.C.)
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China;
- Correspondence: (T.C.); (G.C.)
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45
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Moosavian M, Keshavarzi R, Abbasi Montazeri E, Hajiani E. Loop mediated isothermal amplification of Clostridioides difficile isolates in gastrointestinal patients. AMB Express 2022; 12:42. [PMID: 35412160 PMCID: PMC9005576 DOI: 10.1186/s13568-022-01382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/01/2022] [Indexed: 11/10/2022] Open
Abstract
This study investigated the prevalence of Clostridioides difficile by culture, multiplex polymerase chain reaction (M-PCR), and loop mediated isothermal amplification (LAMP) in patients with suspected C. difficile infections (CDIs). Also, the results of three methods were compared. All stool specimens collected from CDI suspected patients were cultured on selective C. difficile cycloserine-cefoxitin fructose agar and incubated in an anaerobic jar up to 7 days. The bacterial isolates were identified using standard tests. Multiplex-PCR (M-PCR) was performed for detection of tcdA, tcdB, and tpi genes. The LAMP assay was performed to detect the tcdB gene of C. difficile. C. difficile was isolated from 20.0% (n = 10/50) of samples by culture. M-PCR showed that 34.0% (n = 17/50) of the specimens were positive for C. difficile based on the presence of tpi gene. Out of the 17 C. difficile, 13 strains (76.0%) were positive for tcdB gene using M-PCR. However, the LAMP assay showed that 30.0% (15/50) of specimens were positive for the presence of tcdB gene. M-PCR and LAMP methods showed 100.0% sensitivity compared to the culture method. However, the specificity of the LAMP (87.5%) was relatively higher than the M-PCR (82.5%) compared to the culture. Based on the results of this study, the prevalence of toxigenic C. difficile strains was high in suspected CDI patients. So, the differentiation between toxigenic and non-toxigenic strains is necessary. Our data showed that the LAMP assay is a good method for direct detection of toxigenic C. difficile strains from stool specimens.
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DeFina SM, Wang J, Yang L, Zhou H, Adams J, Cushing W, Tuohy B, Hui P, Liu C, Pham K. SaliVISION: a rapid saliva-based COVID-19 screening and diagnostic test with high sensitivity and specificity. Sci Rep 2022; 12:5729. [PMID: 35388102 PMCID: PMC8986854 DOI: 10.1038/s41598-022-09718-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic-caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)– has posed a global threat and presented with it a multitude of economic and public-health challenges. Establishing a reliable means of readily available, rapid diagnostic testing is of paramount importance in halting the spread of COVID-19, as governments continue to ease lockdown restrictions. The current standard for laboratory testing utilizes reverse transcription quantitative polymerase chain reaction (RT-qPCR); however, this method presents clear limitations in requiring a longer run-time as well as reduced on-site testing capability. Therefore, we investigated the feasibility of a reverse transcription looped-mediated isothermal amplification (RT-LAMP)-based model of rapid COVID-19 diagnostic testing which allows for less invasive sample collection, named SaliVISION. This novel, two-step, RT-LAMP assay utilizes a customized multiplex primer set specifically targeting SARS-CoV-2 and a visual report system that is ready to interpret within 40 min from the start of sample processing and does not require a BSL-2 level testing environment or special laboratory equipment. When compared to the SalivaDirect and Thermo Fisher Scientific TaqPath RT-qPCR testing platforms, the respective sensitivities of the SaliVISION assay are 94.29% and 98.28% while assay specificity was 100% when compared to either testing platform. Our data illustrate a robust, rapid diagnostic assay in our novel RT-LAMP test design, with potential for greater testing throughput than is currently available through laboratory testing and increased on-site testing capability.
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Affiliation(s)
- Samuel M DeFina
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jianhui Wang
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Lei Yang
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Han Zhou
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jennifer Adams
- Department of Laboratory Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - William Cushing
- Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA.,Yale New Haven Hospital, New Haven, CT, USA
| | - Beth Tuohy
- Yale University Health Services, Yale University, New Haven, CT, USA
| | - Pei Hui
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA.
| | - Kien Pham
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA.
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Chandrashekar BS, PrasannaKumar MK, Parivallal PB, Pramesh D, Banakar SN, Patil SS, Mahesh HB. Host range and virulence diversity of Pectobacterium carotovorum subsp. brasiliense strain RDKLR infecting radish in India, and development of a LAMP-based diagnostics. J Appl Microbiol 2022; 132:4400-4412. [PMID: 35353430 DOI: 10.1111/jam.15553] [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: 12/16/2021] [Revised: 02/27/2022] [Accepted: 03/26/2022] [Indexed: 11/27/2022]
Abstract
AIM This work aimed at determining the pathogenicity, molecular characterization, host range and rapid detection of Pectobacterium carotovorum subsp. brasiliense (Pcb) causing soft rot disease in radish. METHOD AND RESULTS The four isolated isolates were inoculated to radish, typical soft rot symptoms were observed and Koch's postulates were proved. The most virulent strain RDKLR was morphologically and biochemically distinct. Pcb showed a positive potato soft rot test and elicited hypersensitivity response on Nicotiana tobaccum. The genes Pel2 and pmrA were used for sub-species characterization of Pcb. It has a wide host range and infection was observed on slices of carrot, tomato, cauliflower, cabbage, chili, knol-khol, bell pepper and cucumber. Infectivity was also seen in seedlings under glasshouse conditions. Pcb produced cell wall degrading enzymes in semi-quantification assay and is a strong biofilm producer. The LAMP technique was standardized to help rapid detection and take prophylactic measures to manage the disease. CONCLUSION This work reports Pcb as a new soft rot causing organism of radish in India. Pcb is highly virulent with a broad host range. The LAMP technique helps in rapid detection. SIGNIFICANCE AND IMPACT OF STUDY Pcb-induced soft rot causes significant yield loss, decreased market value, damage in transit, storage, and the market. Disease characterisation and early identification aid in disease management and prevention in the field.
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Affiliation(s)
- B S Chandrashekar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - M K PrasannaKumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - P Buela Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - D Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, Gangavathi, University of Agricultural Sciences, Raichur, India
| | - Sahana N Banakar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - Swathi S Patil
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - H B Mahesh
- Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, Mandya, India
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48
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Dong Y, Zhao Y, Li S, Wan Z, Lu R, Yang X, Yu G, Reboud J, Cooper JM, Tian Z, Zhang C. Multiplex, Real-Time, Point-of-care RT-LAMP for SARS-CoV-2 Detection Using the HFman Probe. ACS Sens 2022; 7:730-739. [PMID: 35192340 PMCID: PMC8887655 DOI: 10.1021/acssensors.1c02079] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/08/2022] [Indexed: 12/11/2022]
Abstract
Viral evolution impacts diagnostic test performance through the emergence of variants with sequences affecting the efficiency of primer binding. Such variants that evade detection by nucleic acid-based tests are subject to selective pressure, enabling them to spread more efficiently. Here, we report a variant-tolerant diagnostic test for SARS-CoV-2 using a loop-mediated isothermal nucleic acid-based amplification (LAMP) assay containing high-fidelity DNA polymerase and a high-fidelity DNA polymerase-medicated probe (HFman probe). In addition to demonstrating a high tolerance to variable SARS-CoV-2 viral sequences, the mechanism also overcomes frequently observed limitations of LAMP assays arising from non-specific amplification within multiplexed reactions performed in a single "pot". Results showed excellent clinical performance (sensitivity 94.5%, specificity 100%, n = 190) when compared directly to a commercial gold standard reverse transcription quantitative polymerase chain reaction assay for the extracted RNA from nasopharyngeal samples and the capability of detecting a wide range of sequences containing at least alpha and delta variants. To further validate the test with no sample processing, directly from nasopharyngeal swabs, we also detected SARS-CoV-2 in positive clinical samples (n = 49), opening up the possibility for the assay's use in decentralized testing.
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Affiliation(s)
- Yajuan Dong
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjuan Zhao
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Shenwei Li
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Zhenzhou Wan
- Medical
Laboratory of Taizhou Fourth People’s Hospital, Taizhou 225300, China
| | - Renfei Lu
- Clinical
Laboratory, Nantong Third Hospital Affiliated
to Nantong University, Nantong 226006, China
| | - Xianguang Yang
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Guoying Yu
- College
of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Julien Reboud
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Jonathan M. Cooper
- Division
of Biomedical Engineering, University of
Glasgow, G12 8LT Glasgow, U.K.
| | - Zhengan Tian
- Shanghai
International Travel Healthcare Center, Shanghai 200335, China
| | - Chiyu Zhang
- Shanghai
Public Health Clinical Center, Fudan University, Shanghai 201508, China
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49
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Nouri R, Dong M, Politza AJ, Guan W. Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison. ACS Sens 2022; 7:900-911. [PMID: 35238530 PMCID: PMC9191621 DOI: 10.1021/acssensors.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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50
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Tran DH, Tran HT, Pham TNM, Phung HTT. Direct multiplex recombinase polymerase amplification for rapid detection of S taphylococcus aureus and P seudomonas aeruginosa in food. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2022; 11:1-10. [PMID: 35463821 PMCID: PMC9012432 DOI: 10.22099/mbrc.2021.41503.1664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Food and beverage poisoning is detrimental to people's health since it can lead to fever, stomachaches, and even death. To rapidly detect the presence of foodborne pathogens, conventional PCR assays are currently widely employed. Meanwhile, isothermal PCR methods, in which the amplification reactions take place at a low and constant temperature, have lately emerged as effective and alternative means for quickly identifying pathogens in low-resource settings. Staphylococcus aureus and Pseudomonas aeruginosa are two of the most concerning foodborne bacterial infections. In this work, an isothermal PCR assay based on the Recombinase Polymerase Amplification (RPA) method was developed to simultaneously detect S. aureus and P. aeruginosa with high sensitivity and specificity. The limit of detection for multiplex RPA was 10 and 30 fg/reaction of S. aureus and P. aeruginosa genomic DNA, respectively. Furthermore, the reaction time was reduced to only 25 minutes, with a low incubation temperature of 39°C. Multiplex RPA reactions, in particular, were successful in directly identifying as low as 1 and 5 CFU/reaction of S. aureus and P. aeruginosa cells, respectively, without the need for DNA genome extraction. Moreover, the multiplex RPA reliably detected the two foodborne bacteria in milk, fruit juice, and bottled water samples. In conclusion, the direct multiplex RPA reported in this work offers a quick, easy, sensitive, and effective alternative approach for detecting the presence of S. aureus and P. aeruginosa without the requirement of a pricey instrument or highly-trained personnel.
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Affiliation(s)
| | | | | | - Huong Thi Thu Phung
- Corresponding Author: NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam. Tel: +84 981411701; Fax: +84 28 39 404 759 E. mail:
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