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Adewusi OO, Waldner CL, Hanington PC, Hill JE, Freeman CN, Otto SJG. Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review. J Vet Diagn Invest 2024; 36:400-417. [PMID: 38456288 PMCID: PMC11110769 DOI: 10.1177/10406387241235968] [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] [Indexed: 03/09/2024] Open
Abstract
Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.
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Affiliation(s)
- Olufunto O. Adewusi
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Cheryl L. Waldner
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Janet E. Hill
- Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Claire N. Freeman
- Departments of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J. G. Otto
- HEAT-AMR (Human-Environment-Animal Transdisciplinary Antimicrobial Resistance) Research Group, University of Alberta, Edmonton, AB, Canada
- Healthy Environments Thematic Area Lead, Centre for Healthy Communities, University of Alberta, Edmonton, AB, Canada
- School of Public Health, University of Alberta, Edmonton, AB, Canada
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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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Abe H, Ushijima Y, Bikangui R, Ondo GN, Moure A, Yali-Assy-Oyamli Y, Yoshikawa R, Lell B, Adegnika AA, Yasuda J. Long-term validation of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 from March 2020 to October 2021 in Central Africa, Gabon. PLoS Negl Trop Dis 2022; 16:e0010964. [PMID: 36455044 DOI: 10.1371/journal.pntd.0010964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/13/2022] [Accepted: 11/19/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Despite the development of several methods for diagnosing COVID-19, long-term validation of such methods remains limited. In the early phase of the COVID-19 pandemic, we developed a rapid and sensitive diagnostic method based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) methodology, which is suitable for point-of-care application or for use in resource-limited settings to detect SARS-CoV-2. To assess the applicability of the RT-LAMP assay technique to resource-limited regions, such as rural areas in Africa, and to verify the usability of the method against various SARS-CoV-2 variants, the method was validated using clinical samples collected longitudinally during the pandemic. METHODOLOGY/PRINCIPAL FINDINGS First, the sensitivity of the RT-LAMP assay for detecting 10 SARS-CoV-2 variants was evaluated using viral RNA samples extracted from cell culture with a portable battery-supported device, resulting in the successful detection of 20-50 copies of the viral genome within 15 min, regardless of the variant. COVID-19 positive samples collected in Gabon between March 2020 and October 2021 were used to evaluate the sensitivity of the assay and to calculate the copy number of the SARS-CoV-2 genome. More than 292 copies of the viral genome were detected with 100% probability within 15 min in almost all tests. CONCLUSIONS This long-term validation study clearly demonstrated the applicability of the RT-LAMP assay for the clinical diagnosis of COVID-19 in resource-limited settings of Africa, such as rural areas in Gabon. The results show the potential of the assay as a promising COVID-19 diagnostic method, especially in rural and remote regions located far from the official diagnosis facilities in urban or semi-urban areas.
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Affiliation(s)
- Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Yuri Ushijima
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | | | | | - Ayong Moure
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | | | - Rokusuke Yoshikawa
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Medical University of Vienna, Vienna, Austria
| | - Ayola A Adegnika
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research, Tübingen, Germany
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
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Hu WW, He JW, Guo SL, Li J. Development and evaluation of a rapid and sensitive multienzyme isothermal rapid amplification with a lateral flow dipstick assay for detection of Acinetobacter baumannii in spiked blood specimens. Front Cell Infect Microbiol 2022; 12:1010201. [PMID: 36339332 PMCID: PMC9626983 DOI: 10.3389/fcimb.2022.1010201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Purpose This study aimed to establish the multienzyme isothermal rapid amplification with a lateral flow dipstick (MIRA-LFD) assay and evaluate its performance in detection of A. baumannii in spiked blood specimens. Methods The study was divided into two stages: a pilot study to establish the methodology and a clinical validation study to evaluate its performance. In the first step, we designed primers specific to detect A. baumannii, optimized the MIRA-LFD assay and analyzed its performance regarding limits of detection, reproducibility, specificity, and efficiency of detection using real-time PCR method. In the second step, we obtained 50 spiked blood isolates and detected these pathogens by MIRA-LFD assay. The MIRA-LFD time was 15 min from DNA sample amplification to complete pathogen detection. Results The developed MIRA-LFD assay displayed a detection limit of 6 CFU/mL for detecting A. baumannii, which was significantly better than that of real-time PCR method, and no cross-reactivity was observed in other non-A. baumannii studied. The results obtained with 50 spiked blood isolates suggested that the developed MIRA-LFD assay had high specificity and sensitivity for identifying A. baumannii. Conclusions This study demonstrates that the established MIRA-LFD assay is time-saving, more effective and sensitive, which may become a powerful tool for rapid and reliable diagnosis of bloodstream infection caused by A. baumannii in primary hospitals.
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Affiliation(s)
- Wei-Wei Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jian-Wei He
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Shu-Liang Guo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Jin Li, ; Shu-Liang Guo,
| | - Jin Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
- *Correspondence: Jin Li, ; Shu-Liang Guo,
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González-López A, Cima-Cabal MD, Rioboó-Legaspi P, Costa-Rama E, García-Suárez MDM, Fernández-Abedul MT. Electrochemical Detection for Isothermal Loop-Mediated Amplification of Pneumolysin Gene of Streptococcus pneumoniae Based on the Oxidation of Phenol Red Indicator. Anal Chem 2022; 94:13061-13067. [PMID: 36106671 PMCID: PMC9523611 DOI: 10.1021/acs.analchem.2c02127] [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] [Indexed: 11/28/2022]
Abstract
![]()
A highly sensitive electrochemical methodology for end-point detection
of loop-mediated isothermal nucleic acid amplification reactions was
developed. It is based on the oxidation process of phenol red (PR),
commonly used as a visual indicator. The dependence of its redox process
on pH, which changes during amplification, allows performing quantitative
measurements. Thus, the change in the oxidation potential of PR during
the amplification is used, for the first time, as the analytical signal
that correlates with the number of initial DNA copies. As a proof-of-concept,
the amplification of the pneumolysin gene from Streptococcus
pneumoniae, one of the main pathogens causing community-acquired
pneumonia, is performed. Combination of isothermal amplification with
electrochemical detection, performed on small-size flexible electrodes,
allows easy decentralization. Adaptation to the detection of other
pathogens causing infectious diseases would be very useful in the
prevention of future epidemics.
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Affiliation(s)
- Andrea González-López
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | - María Dolores Cima-Cabal
- Escuela Superior de Ingeniería y Tecnología, Universidad Internacional de La Rioja, Avda. de La Paz 137, Logroño 26006, Spain
| | - Pablo Rioboó-Legaspi
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | - Estefanía Costa-Rama
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
| | | | - M. Teresa Fernández-Abedul
- Departamento de Química Física y Analítica, Universidad de Oviedo, Avda. Julián Clavería 8, Oviedo 33006, Spain
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Guo YL, Wang SS, Jiang GL, Ban WJ, Liu Y. Evaluation of the diagnostic value of loop-mediated isothermal amplification assays targeting three different Mycobacterium tuberculosis genes. J Microbiol Methods 2022; 200:106547. [PMID: 35926680 DOI: 10.1016/j.mimet.2022.106547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/16/2022] [Accepted: 07/29/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND The aim of the study was to evaluate a loop-mediated isothermal amplification (LAMP) assay for the ability to diagnose tuberculosis directly from clinical samples rapidly. METHODS LAMP assays were performed using previously reported primer sets to amplify three specific Mycobacterium tuberculosis (MTB) gene targets, hspX, gyrB, and IS6110. Quantitated DNA from strain H37Rv were detected for assessment of analytical sensitivity; specificity was evaluated by testing eight species of non-tuberculosis Mycobacterium (NTM) and four unrelated bacterial species. Sputum samples from 68 pulmonary tuberculosis patients and a control group consisting of 45 lung cancer patients and 20 healthy controls were analyzed using LAMP assays, and then compared with smear, culture and quantitative real-time PCR (qRT-PCR) methods. RESULTS All three LAMP assays showed 100% specificity for MTB when tested against NTM and other bacterial species. The gyrB-LAMP assay was able to detect 60 cfu/ml of H37Rv suspension within 1 h, similar to qRT-PCR, but 10 times more sensitive than the hspX-LAMP and IS6110-LAMP assays. In clinical samples, when qRT-PCR was used as the reference method, the sensitivity of the three LAMP assays targeting hspX, gyrB, and IS6110 genes was 94.6, 98.2 and 92.9%, respectively. CONCLUSIONS LAMP is more sensitive than smear microscopy and close to qRT-PCR in sensitivity for the detection of MTB. LAMP has comparable specificity to qRT-PCR but was more rapid and convenient.
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Affiliation(s)
- Yan-Ling Guo
- Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Sai-Sai Wang
- Disease Prevention and Control Department, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China
| | - Guang-Lu Jiang
- National Tuberculosis Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China
| | - Wu-Juan Ban
- Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Yang Liu
- Disease Prevention and Control Department, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China.
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Căpățînă D, Feier B, Hosu O, Tertiș M, Cristea C. Analytical methods for the characterization and diagnosis of infection with Pseudomonas aeruginosa: A critical review. Anal Chim Acta 2022; 1204:339696. [DOI: 10.1016/j.aca.2022.339696] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/05/2022] [Accepted: 03/06/2022] [Indexed: 12/11/2022]
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Poirier AC, Kuang D, Siedler BS, Borah K, Mehat JW, Liu J, Tai C, Wang X, van Vliet AHM, Ma W, Jenkins DR, Clark J, La Ragione RM, Qu J, McFadden J. Development of Loop-Mediated Isothermal Amplification Rapid Diagnostic Assays for the Detection of Klebsiella pneumoniae and Carbapenemase Genes in Clinical Samples. Front Mol Biosci 2022; 8:794961. [PMID: 35223985 PMCID: PMC8864245 DOI: 10.3389/fmolb.2021.794961] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022] Open
Abstract
Klebsiella pneumoniae is an important pathogenic bacterium commonly associated with human healthcare and community-acquired infections. In recent years, K. pneumoniae has become a significant threat to global public and veterinary health, because of its high rates of antimicrobial resistance (AMR). Early diagnosis of K. pneumoniae infection and detection of any associated AMR would help to accelerate directed therapy and reduce the risk of the emergence of multidrug-resistant isolates. In this study, we identified three target genes (yhaI, epsL, and xcpW) common to K. pneumoniae isolates from both China and Europe and designed loop-mediated isothermal amplification (LAMP) assays for the detection of K. pneumoniae in clinical samples. We also designed LAMP assays for the detection of five AMR genes commonly associated with K. pneumoniae. The LAMP assays were validated on a total of 319 type reference strains and clinical isolates of diverse genetic backgrounds, in addition to 40 clinical human sputum samples, and were shown to be reliable, highly specific, and sensitive. For the K. pneumoniae–specific LAMP assay, the calculated sensitivity, specificity, and positive and negative predictive values (comparison with culture and matrix-assisted laser desorption/ionization–time of flight mass spectrometry) were all 100% on clinical isolates and, respectively, of 100%, 91%, and 90%, and 100% when tested on clinical sputum samples, while being significantly faster than the reference methods. For the blaKPC and other carbapenemases’ LAMP assays, the concordance between the LAMP results and the references methods (susceptibility tests) was 100%, on both pure cultures (n = 125) and clinical samples (n = 18). In conclusion, we developed highly sensitive and specific LAMP assays for the clinical identification of K. pneumoniae and detection of carbapenem resistance.
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Affiliation(s)
- Aurore C. Poirier
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Dai Kuang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, School of Medicine, Institute of Respiratory Diseases, Shanghai Jiao Tong University, Shanghai, China
| | - Bianca S. Siedler
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Khushboo Borah
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Jai W. Mehat
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Centre for Microbial Genomics and Animal Microbiome Research, Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Jialin Liu
- Department of Critical Care Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Wang
- Department of Critical Care Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Arnoud H. M. van Vliet
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- Centre for Microbial Genomics and Animal Microbiome Research, Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - David R. Jenkins
- Department of Medical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - John Clark
- Department of Medical Microbiology, Epsom and St Helier University Hospitals NHS Trust, Carshalton, United Kingdom
| | - Roberto M. La Ragione
- Department of Pathology and Infectious Diseases, Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, School of Medicine, Institute of Respiratory Diseases, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Jieming Qu, ; Johnjoe McFadden,
| | - Johnjoe McFadden
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- *Correspondence: Jieming Qu, ; Johnjoe McFadden,
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Garg N, Ahmad FJ, Kar S. Recent advances in loop-mediated isothermal amplification (LAMP) for rapid and efficient detection of pathogens. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100120. [PMID: 35909594 PMCID: PMC9325740 DOI: 10.1016/j.crmicr.2022.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/18/2022] [Accepted: 02/20/2022] [Indexed: 11/01/2022] Open
Abstract
Significance of LAMP method in rapid disease diagnosis is highlighted. Different detection methods for amplicon visualization are explained. Advancements in LAMP technique for disease identification are summarized. Trends in development of LAMP disease diagnosis are discussed.
Loop-mediated isothermal amplification (LAMP) method has been demonstrated to bea reliable and robust method for detection and identification of viral and microbial pathogens. LAMP method of amplification, coupled with techniques for easy detection of amplicons, makes a simple-to-operate and easy-to-read molecular diagnostic tool for both laboratory and on-field settings. Several LAMP-based diagnostic kits and assays have been developed that are specifically targeted against a variety of pathogens. With the growing needs of the demanding molecular diagnostic industry, many technical advances have been made over the years by combining the basic LAMP principle with several other molecular approaches like real-time detection, multiplex methods, chip-based assays.This has resulted in enhancing thethe sensitivity and accuracy of LAMP for more rigorous and wide-ranging pathogen detection applications. This review summarizes the current developments in LAMP technique and their applicability in present and future disease diagnosis.
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Zhang H, Xie W, Liu J, Xiang X, Zhang S, Hu J, Yang J. Systematic Study on a Quantitative Analysis of Multicomponents by Single Marker (QAMS) Method for Simultaneous Determination of Eight Constituents in Pneumonia Mixture by UPLC-MS/MS. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2021; 2021:8311588. [PMID: 34777891 PMCID: PMC8580625 DOI: 10.1155/2021/8311588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Pneumonia mixture was formulated and is available to treat children acute pneumonia and acute bronchitis in our hospital for nearly forty years, but there are few studies of its quality evaluation or control. In this paper, a new strategy for quality evaluation of pneumonia mixture was explored and verified through qualitative and quantitative analyses of multicomponents by single marker (QAMS) by UPLC-MS/MS. Baicalein was selected as an internal reference, and the relative correction factors (RCFs) and the relative retention time (RRT) of (R, S)-goitrin, amygdalin, chlorogenic acid, pseudoephedrine hydrochloride, ephedrine hydrochloride, ammonium glycyrrhizinate, and baicalin were established. The robustness and durability of the QAMS method were investigated. RCF values calculated by the average (AVG) method and linear regression (LRG) method had good repeatability and were acceptable for quantitative analysis, and the RTT combined with the exact masses of precursor and fragment ions and their abundance could be adopted for accurately positioning the chromatographic peak of the eight constituents. The consistency and feasibility of the QAMS method were verified by comparing the contents of the seven components calculated by a classic and validated external standard method (ESM) with those of the QAMS method, which reduces analytical cost and time of detection and avoids the problem of the diversity and large quantity of reference standards. The results demonstrated that the QAMS method developed in this paper could provide a new, alternative, and promising method to comprehensively and effectively determine multicomponents and control the quality of pneumonia mixture or even a group of similar medicines.
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Affiliation(s)
- Haibo Zhang
- College of Pharmacy, Xinjiang Medical University, Urumqi 830011, China
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Weina Xie
- College of Pharmacy, Xinjiang Medical University, Urumqi 830011, China
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
| | - Jiangyun Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Xiaoqiang Xiang
- Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shilei Zhang
- College of Pharmacy, Xinjiang Medical University, Urumqi 830011, China
| | - Junping Hu
- College of Pharmacy, Xinjiang Medical University, Urumqi 830011, China
| | - Jianhua Yang
- College of Pharmacy, Xinjiang Medical University, Urumqi 830011, China
- Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830011, China
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Nesakumar N, Lakshmanakumar M, Srinivasan S, Jayalatha JBB A, Balaguru Rayappan JB. Principles and Recent Advances in Biosensors for Pathogens Detection. ChemistrySelect 2021. [DOI: 10.1002/slct.202101062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Noel Nesakumar
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Chemical and Biotechnology SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Muthaiyan Lakshmanakumar
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Soorya Srinivasan
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Arockia Jayalatha JBB
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - John Bosco Balaguru Rayappan
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
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Vergara A, Moreno-Morales J, Roca I, Pitart C, Kostyanev T, Rodriguez-Baño J, Goossens H, Marco F, Vila J. A comparative study between real-time PCR and loop-mediated isothermal amplification to detect carbapenemase and/or ESBL genes in Enterobacteriaceae directly from bronchoalveolar lavage fluid samples. J Antimicrob Chemother 2021; 75:1453-1457. [PMID: 32073602 DOI: 10.1093/jac/dkaa031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES To evaluate and compare the efficacy of real-time PCR (Xpert Carba-R) and loop-mediated isothermal amplification (Eazyplex® SuperBug CRE) for detecting carbapenemase carriage in Enterobacteriaceae directly from bronchoalveolar lavage (BAL). METHODS Negative BAL samples were spiked with 21 well-characterized carbapenemase-producing Enterobacteriaceae strains to a final concentration of 102-104 cfu/mL. Xpert Carba-R (Cepheid, Sunnyvale, CA, USA), which detects five targets (blaKPC, blaNDM, blaVIM, blaOXA-48 and blaIMP-1), and the Eazyplex® SuperBug CRE system (Amplex-Diagnostics GmbH, Germany), which detects seven genes (blaKPC, blaNDM, blaVIM, blaOXA-48, blaOXA-181, blaCTXM-1 and blaCTXM-9), were evaluated for the detection of these genes directly from BAL samples. RESULTS Xpert Carba-R showed 100% agreement with carbapenemase characterization by PCR and sequencing for all final bacteria concentrations. Eazyplex® SuperBug CRE showed 100%, 80% and 27% agreement with PCR and sequencing when testing 104, 103 and 102 cfu/mL, respectively. False negative results for Eazyplex® SuperBug CRE matched the highest cycle threshold values for Xpert Carba-R. Hands-on time for both assays was about 15 min, but Eazyplex® SuperBug CRE results were available within 30 min, whereas Xpert Carba-R took around 50 min. CONCLUSIONS We here describe the successful use of two commercial diagnostic tests, Xpert Carba-R and Eazyplex® SuperBug CRE, to detect bacterial carbapenem resistance genes directly in lower respiratory tract samples. Our results could be used as proof-of-concept data for validation of these tests for this indication.
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Affiliation(s)
- A Vergara
- Department of Clinical Microbiology - CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - J Moreno-Morales
- Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - I Roca
- Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - C Pitart
- Department of Clinical Microbiology - CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - T Kostyanev
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - J Rodriguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena/Departamento de Medicina, Universidad de Sevilla/Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - H Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.,Laboratory of Medical Microbiology, University Hospital Antwerp, Antwerp, Belgium
| | - F Marco
- Department of Clinical Microbiology - CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain.,Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - J Vila
- Department of Clinical Microbiology - CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain.,Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen of significant concern to susceptible patient populations. This pathogen can cause nosocomial and community-acquired respiratory and bloodstream infections and various other infections in humans. Sources include water, plant rhizospheres, animals, and foods. Studies of the genetic heterogeneity of S. maltophilia strains have identified several new genogroups and suggested adaptation of this pathogen to its habitats. The mechanisms used by S. maltophilia during pathogenesis continue to be uncovered and explored. S. maltophilia virulence factors include use of motility, biofilm formation, iron acquisition mechanisms, outer membrane components, protein secretion systems, extracellular enzymes, and antimicrobial resistance mechanisms. S. maltophilia is intrinsically drug resistant to an array of different antibiotics and uses a broad arsenal to protect itself against antimicrobials. Surveillance studies have recorded increases in drug resistance for S. maltophilia, prompting new strategies to be developed against this opportunist. The interactions of this environmental bacterium with other microorganisms are being elucidated. S. maltophilia and its products have applications in biotechnology, including agriculture, biocontrol, and bioremediation.
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Moreno-Morales J, Vergara A, Kostyanev T, Rodriguez-Baño J, Goossens H, Vila J. Evaluation of a Loop-Mediated Isothermal Amplification Assay to Detect Carbapenemases Directly From Bronchoalveolar Lavage Fluid Spiked With Acinetobacter spp. Front Microbiol 2021; 11:597684. [PMID: 33519735 PMCID: PMC7838357 DOI: 10.3389/fmicb.2020.597684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
Carbapenem-resistant Acinetobacter spp. mainly Acinetobacter baumannii are frequently causing nosocomial infections with high mortality. In this study, the efficacy of the Eazyplex® SuperBug Complete A system, based on loop-mediated isothermal amplification (LAMP), to detect the presence of carbapenemases in Acinetobacter spp. directly from bronchoalveolar lavage (BAL) samples was assessed. A total of 22 Acinetobacter spp. strains producing OXA-23, OXA-40, OXA-58, NDM, and IMP were selected. Eazyplex SuperBug Complete A kit, used with the Genie II device, is a molecular diagnostics kit that detects a selection of genes that express carbapenemases (bla KPC , bla NDM , bla VIM , bla OXA-48 , bla OXA-23 , bla OXA-40 , and bla OXA-58 ). Negative BAL samples were identified, McFarland solutions were prepared from each of the 22 Acinetobacter strains and serial dilutions in saline solution were made to finally spike BAL samples to a concentration of 102 and 103 CFU/ml. Fifteen concentrations out of the 44 tested out did not provide detection of the carbapenemase-producing gene, all but one being at the lowest concentration tested at 102 CFU/ml; therefore, the limit of sensitivity is 103 CFU/ml. This assay represents the kind of advantages that investing in molecular diagnostics brings to the clinical practice, allowing the identification of carbapenemases in less than 30 min with a sensitivity of 103 CFU/ml.
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Affiliation(s)
- Javier Moreno-Morales
- Institute for Global Health (ISGlobal), Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology – CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Tomislav Kostyanev
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Jesús Rodriguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena/Departamento de Medicina, Universidad de Sevilla/Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
| | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Laboratory of Medical Microbiology, University Hospital Antwerp, Antwerp, Belgium
| | - Jordi Vila
- Institute for Global Health (ISGlobal), Hospital Clínic – Universitat de Barcelona, Barcelona, Spain
- Department of Clinical Microbiology – CDB, Hospital Clínic, University of Barcelona, Barcelona, Spain
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Lei J, Han X, Tang X, Wang H, Zhang Q. Development of Anti-Idiotypic Nanobody-Phage Based Immuno-Loop-Mediated Isothermal Amplification Assay for Aflatoxins in Peanuts. Toxins (Basel) 2020; 12:toxins12090565. [PMID: 32887280 PMCID: PMC7551471 DOI: 10.3390/toxins12090565] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/20/2023] Open
Abstract
Aflatoxin contamination in agricultural products has posed serious health hazards and brought huge economic loss in the food and feed industries. Monitoring aflatoxins in various foods and feeds has become a crucial means to protect public health. This study aimed to report an immuno-loop-mediated isothermal amplification (iLAMP) assay by using an anti-idiotypic nanobody-phage for on-site and rapid detection of aflatoxin in real samples. The iLAMP method was developed on the basis of a competitive immunoassay and LAMP reaction performed in a simple water bath. This method can provide visualized test results: violet color represents positive samples while sky blue represents negative. The visual detection limits of iLAMP for aflatoxin B1, B2, G1, and G2 in peanut samples were 1.6, 1.6, 3.2, and 16 μg/kg, respectively. The developed assay was verified with high performance liquid chromatography (HPLC) for the analysis of aflatoxins in peanuts, which demonstrated that the iLAMP method can be applied to the detection of aflatoxin in real samples. The novel iLAMP assay eliminates the need for aflatoxin conjugates, the antibody labeling process, and special equipment, and offers an alternative to existing methods with advantages of time-saving, cost-effectiveness, and ease-of-use.
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Affiliation(s)
- Jiawen Lei
- College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (J.L.); (H.W.)
| | - Xiaole Han
- College of Chemistry and Material Sciences, South-Central University for Nationalities, Wuhan 430074, China;
| | - Xiaoqian Tang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
| | - Haiying Wang
- College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China; (J.L.); (H.W.)
| | - Qi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
- Correspondence: ; Tel.: +86-27-8681-2943
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Liao W, Long D, Huang Q, Wei D, Liu X, Wan L, Feng Y, Zhang W, Liu Y. Rapid Detection to Differentiate Hypervirulent Klebsiella pneumoniae (hvKp) From Classical K. pneumoniae by Identifying peg-344 With Loop-Mediated Isothermal Amplication (LAMP). Front Microbiol 2020; 11:1189. [PMID: 32655515 PMCID: PMC7325879 DOI: 10.3389/fmicb.2020.01189] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022] Open
Abstract
Objectives To establish a rapid molecular diagnostics of hvKp using the peg-344 loop-mediated isothermal amplification technique (LAMP). Methods In all, 28 K. pneumoniae strains isolated from the blood of patients were used for the peg-344 LAMP. K. pneumoniae NTUH-K2044 and K. pneumoniae ATCC700603 were used as positive control and negative control, respectively. For comparison, all the results were detected in a polymerase chain reaction (PCR), which was considered the gold standard for the detection of the gene. Mouse lethality assay, and Serum killing assay were also used to determine the virulence phenotype of K. pneumoniae. Results We determined the specificity and sensitivity of the primers for peg-344 detection in the LAMP reactions. This LAMP assay was able to specifically differentiate hvKp from classical K. pneumoniae (cKp) at 65°C, which was 100-fold more sensitive than a PCR assay for peg-344 detection. The virulence phenotype of K. pneumoniae detected by LAMP was as precise as by Mouse lethality assay and Serum killing assay. Conclusion The LAMP assay is easy to perform and rapid. Therefore, it can be routinely applied to differentiate hvKp from cKp in the clinical laboratory.
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Affiliation(s)
- Wenjian Liao
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dan Long
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qisen Huang
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dandan Wei
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaobing Liu
- Department of Endocrinology Medicine, The Third Hospital of Nanchang, Nanchang, China
| | - Lagen Wan
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yuling Feng
- Medicine College, Nanchang University, Nanchang, China
| | - Wei Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yang Liu
- Department of Clinical Microbiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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