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Ahortor EK, Gwira TM, Mahazu S, Erber AC, Ablordey A. Evaluation of an electricity-independent method for IS2404 Loop-mediated isothermal amplification (LAMP) diagnosis of Buruli ulcer in resource-limited settings. PLoS Negl Trop Dis 2024; 18:e0012338. [PMID: 39141676 PMCID: PMC11346967 DOI: 10.1371/journal.pntd.0012338] [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: 12/01/2023] [Revised: 08/26/2024] [Accepted: 07/04/2024] [Indexed: 08/16/2024] Open
Abstract
INTRODUCTION Buruli ulcer (BU) caused by Mycobacterium ulcerans (MU) is a devastating necrotic skin disease. PCR, recommended for confirmation of BU by WHO, requires an adequately equipped laboratory, therefore often delaying timely diagnosis and treatment of BU patients in remote settings. Loop-mediated isothermal amplification (LAMP) is a PCR-based protocol for isothermal amplification of DNA that has been suggested for diagnosis of BU in low-resource settings. STUDY AIMS AND METHODS This is an exploratory diagnostic test evaluation study, with an embedded qualitative sub-study. Its aims are two-fold: First, to evaluate a simple rapid syringe-based DNA extraction method (SM) in comparison with a more elaborate conventional DNA extraction method (CM), followed by a LAMP assay targeting IS2404 for the detection of MU, either using a commercially available pocket warmer (pw) or a heat block (hb) for incubation. Second, to complement this by exploring the diagnostic workflow for BU at a community-based health centre in an endemic area in rural Ghana as an example of a potential target setting, using interviews with researchers and health care workers (HCWs). Diagnostic test evaluation results are discussed in relation to the requirements of a target product profile (TPP) for BU diagnosis and the target setting. RESULTS A protocol using SM for DNA extraction followed by IS2404 PCR (IS2404 PCRSM) was able to identify MU DNA in 73 out of 83 BU clinical specimens submitted for diagnosis. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of IS2404 PCRSM were 90.12%, 100%, 100% and 65.21% respectively, as compared to the reference standard IS2404 PCR in combination with a standard extraction protocol for mycobacterial DNA. Evaluation of the LAMP assay on 64 SM DNA extracts showed a sensitivity, specificity, PPV and NPV of 83.6%, 100%, 100% and 50%, respectively, using either pocket warmer (pwLAMPSM) or heat block (hbLAMPSM) for incubation of the reaction, as compared to the same reference standard. The limit of detection of pwLAMPSM was found to be 30 copies of the IS2404 target. Interview findings explored barriers to BU diagnosis and treatment, including perceptions of the disease, costs, and availability of transport. Participants confirmed that a diagnosis at the PoC, in addition to screening based on clinical criteria, would be advantageous in order to prevent delays and loss to follow-up. DISCUSSION AND CONCLUSIONS The high diagnostic and analytic accuracy of the pwLAMP, evaluated by us in combination with a syringe-based DNA extraction method, supports its potential use for the rapid detection of MU in suspected BU samples at the community or primary health care level without reliable electricity supply. Further optimization needs include a lysis buffer, evaluation directly at the PoC and/or other sites, assessing staff training requirements and quality control.
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Affiliation(s)
- Evans K. Ahortor
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- School of Pharmacy and Pharmaceutical Science, Cardiff University, Cardiff, Wales, United Kingdom
| | - Theresa Manful Gwira
- Department of Biochemistry, Cell and Molecular Biology & West African Centre for Cell Biology of Infectious Pathogens, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Samiratu Mahazu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Astrid C. Erber
- Department of Epidemiology, Centre for Public Health, Medical University of Vienna, Vienna, Austria
- Infectious Diseases Data Observatory, Oxford, United Kingdom
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
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Shkodenko LA, Mohamed AA, Ateiah M, Rubel MS, Koshel EI. A DAMP-Based Assay for Rapid and Affordable Diagnosis of Bacterial Meningitis Agents: Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae. Int J Mol Sci 2024; 25:8282. [PMID: 39125852 PMCID: PMC11311791 DOI: 10.3390/ijms25158282] [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: 07/08/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The rapid and accurate diagnosis of meningitis is critical for preventing severe complications and fatalities. This study addresses the need for accessible diagnostics in the absence of specialized equipment by developing a novel diagnostic assay. The assay utilizes dual-priming isothermal amplification (DAMP) with unique internal primers to significantly reduce non-specificity. For fluorescence detection, the dye was selected among Brilliant Green, Thioflavin T, and dsGreen. Brilliant Green is preferred for this assay due to its availability, high fluorescence level, and optimal sample-to-background (S/B) ratio. The assay was developed for the detection of the primary causative agents of meningitis (Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae), and tested on clinical samples. The developed method demonstrated high specificity, no false positives, sensitivity comparable to that of loop-mediated isothermal amplification (LAMP), and a high S/B ratio. This versatile assay can be utilized as a standalone test or an integrated assay into point-of-care systems for rapid and reliable pathogen detection.
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Affiliation(s)
| | | | | | | | - Elena I. Koshel
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Lomonosova Street, 9, 191002 St Petersburg, Russia; (L.A.S.); (A.-A.M.); (M.A.); (M.S.R.)
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3
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Nar Otgun S, Ketre Kolukirik CZ, Unal Sahin N, Kolukirik M, Girgin Ozgumus G, Turan M, Elmas M, Kilic S. Enhancing sensitivity of qPCR assays targeting Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae by using a mutant Taq DNA polymerase. J Microbiol Methods 2024; 219:106899. [PMID: 38360298 DOI: 10.1016/j.mimet.2024.106899] [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: 12/13/2023] [Revised: 01/19/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
AIMS Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae are important causes of bacterial meningitis. In this study, the DNA binding site of the wild type Taq DNA polymerase was modified to produce a mutant enzyme with enhanced DNA affinity and PCR performance. The engineered and the wild type enzymes were integrated into qPCR-based assays for molecular detection of S. pneumoniae, N. meningitidis, H. influenzae, and serogroups and serotypes of these three pathogens. METHODS Bio-Speedy® Bacterial DNA Isolation Kit (Bioeksen R&D Technologies, Turkiye) and 2× qPCR-Mix for hydrolysis probes (Bioeksen R&D Technologies, Turkiye) and CFX96 Instrument (Biorad Inc., USA) were used for all molecular analyses. Spiked negative clinical specimens were tested using the developed qPCR assays and the culture-based conventional methods for the analytical performance evaluation. RESULTS All qPCR assays did not produce any positive results for the samples spiked with potential cross-reacting bacteria. Limit of detection (LOD) of the assays containing the mutant enzyme was 1 genome/reaction (10 cfu/mL sample) which is at least 3 times lower than the previously reported LOD levels for DNA amplification based molecular assays. LODs for the spiked serum and cerebrospinal fluid (CSF) samples decreased 2.3-4.7 and 1.2-3.5 times respectively when the mutant enzyme was used instead of the wild type Taq DNA polymerase. CONCLUSIONS It is possible to enhance analytical sensitivity of qPCR assays targeting the bacterial agents of meningitis by using an engineered Taq DNA polymerase. These qPCR-based assays can be used for direct detection and serogrouping / serotyping of S. pneumoniae, N. meningitidis and H. influenzae at concentrations close to the lower limit of medical decision point.
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Affiliation(s)
- Selin Nar Otgun
- Public Health General Directorate, Microbiology Reference Laboratories and Biological Products Department, Ankara, Turkiye.
| | | | - Nuriye Unal Sahin
- Public Health General Directorate, Microbiology Reference Laboratories and Biological Products Department, Ankara, Turkiye
| | - Mustafa Kolukirik
- Bioeksen R&D Technologies Ltd., Istanbul Technical University Ari-3 Technopark, Istanbul, Turkiye
| | - Gozde Girgin Ozgumus
- Bioeksen R&D Technologies Ltd., Istanbul Technical University Ari-3 Technopark, Istanbul, Turkiye
| | - Meral Turan
- Public Health General Directorate, Microbiology Reference Laboratories and Biological Products Department, Ankara, Turkiye
| | - Mert Elmas
- Bioeksen R&D Technologies Ltd., Istanbul Technical University Ari-3 Technopark, Istanbul, Turkiye
| | - Selcuk Kilic
- Health Sciences University, Defence Health Sciences Institute, Ankara, Turkiye
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Peela SCM, Sistla S. Utility of quantitative loop mediated isothermal amplification (qLAMP) assay for the diagnosis of invasive pneumococcal disease (IPD). Indian J Med Microbiol 2024; 48:100575. [PMID: 38537871 DOI: 10.1016/j.ijmmb.2024.100575] [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: 12/21/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 05/08/2024]
Abstract
PURPOSE Quantitative LAMP (qLAMP) assay is one of the recent and emerging diagnostic tests for infectious diseases. Only a few studies exist comparing this assay with quantitative real-time PCR (qPCR) for the diagnosis of invasive pneumococcal disease (IPD). AIM To compare the diagnostic performance of qLAMP assay with qPCR targeting autolysin gene for the diagnosis of invasive pneumococcal disease. METHODS Ninety six blood samples and 73 CSF samples from patients clinically suspected with community acquired pneumonia and acute meningitis were tested by qPCR and qLAMP assays using previously published primers and protocols. The qPCR was considered as the gold standard test and the diagnostic performance was assessed by calculating sensitivity, specificity, positive and negative predictive values, and kappa coefficient for the level of agreement between the tests. Chi-squared/Fisher exact test was used to compare categorical variables (positive/negative). RESULTS Thirty two blood samples and 22 CSF samples were positive by qPCR while 24 and 20 samples were positive by qLAMP assay respectively. The sensitivity of qLAMP assay was only 86.4% and 75% when tested on CSF and blood samples respectively. However, the qLAMP assay was in substantial to almost perfect agreement when compared with qPCR. The results were statistically significant in both sample types (P < 0.001). CONCLUSIONS The performance of qLAMP assay can vary based on the specimen type. It has very high specificity and had substantial to almost perfect agreement, and thus may be an alternative to qPCR for the diagnosis of IPD.
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Affiliation(s)
- Sreeram Chandra Murthy Peela
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India.
| | - Sujatha Sistla
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India.
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Cao WF, Leng EL, Liu SM, Zhou YL, Luo CQ, Xiang ZB, Cai W, Rao W, Hu F, Zhang P, Wen A. Recent advances in microbiological and molecular biological detection techniques of tuberculous meningitis. Front Microbiol 2023; 14:1202752. [PMID: 37700862 PMCID: PMC10494440 DOI: 10.3389/fmicb.2023.1202752] [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: 04/10/2023] [Accepted: 07/21/2023] [Indexed: 09/14/2023] Open
Abstract
Tuberculous meningitis (TBM) is the most common type of central nervous system tuberculosis (TB) and has the highest mortality and disability rate. Early diagnosis is key to improving the prognosis and survival rate of patients. However, laboratory diagnosis of TBM is often difficult due to its paucibacillary nature and sub optimal sensitivity of conventional microbiology and molecular tools which often fails to detect the pathogen. The gold standard for TBM diagnosis is the presence of MTB in the CSF. The recognised methods for the identification of MTB are acid-fast bacilli (AFB) detected under CSF smear microscopy, MTB cultured in CSF, and MTB detected by polymerase chain reaction (PCR). Currently, many studies consider that all diagnostic techniques for TBM are not perfect, and no single technique is considered simple, fast, cheap, and efficient. A definite diagnosis of TBM is still difficult in current clinical practice. In this review, we summarise the current state of microbiological and molecular biological diagnostics for TBM, the latest advances in research, and discuss the advantages of these techniques, as well as the issues and challenges faced in terms of diagnostic effectiveness, laboratory infrastructure, testing costs, and clinical expertise, for clinicians to select appropriate testing methods.
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Affiliation(s)
- Wen-Feng Cao
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Er-Ling Leng
- Department of Pediatrics, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
| | - Shi-Min Liu
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Yong-Liang Zhou
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Chao-Qun Luo
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Zheng-Bing Xiang
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Wen Cai
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Wei Rao
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Fan Hu
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - Ping Zhang
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, China
| | - An Wen
- Department of Neurology, Jiangxi Provincial People’s Hospital (The First Affiliated Hospital of Nanchang Medical College), Nanchang, Jiangxi, China
- Department of neurology, Xiangya Hospital, Central South University, Jiangxi Hospital, National Regional Center for Neurological Diseases, Nanchang, Jiangxi, 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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Tavakoli H, Hirth E, Luo M, Sharma Timilsina S, Dou M, Dominguez DC, Li X. A microfluidic fully paper-based analytical device integrated with loop-mediated isothermal amplification and nano-biosensors for rapid, sensitive, and specific quantitative detection of infectious diseases. LAB ON A CHIP 2022; 22:4693-4704. [PMID: 36349548 PMCID: PMC9701502 DOI: 10.1039/d2lc00834c] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Bacterial meningitis, an infection of the membranes (meninges) and cerebrospinal fluid (CSF) surrounding the brain and spinal cord, is one of the major causes of death and disability worldwide. Higher case-fatality rates and short survival times have been reported in developing countries. Hence, a quick, straightforward, and low-cost approach is in great demand for the diagnosis of meningitis. In this research, a microfluidic fully paper-based analytical device (μFPAD) integrated with loop-mediated isothermal amplification (LAMP) and ssDNA-functionalized graphene oxide (GO) nano-biosensors was developed for the first time for a simple, rapid, low-cost, and quantitative detection of the main meningitis-causing bacteria, Neisseria meningitidis (N. meningitidis). The results can be successfully read within 1 hour with the limit of detection (LOD) of 6 DNA copies per detection zone. This paper device also offers versatile functions by providing a qualitative diagnostic analysis (i.e., a yes or no answer), confirmatory testing, and quantitative analysis. These features make the presented μFPAD capable of a simple, highly sensitive, and specific diagnosis of N. meningitis. Furthermore, this microfluidic approach has great potential in the rapid detection of a wide variety of different other pathogens in low-resource settings.
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Affiliation(s)
- Hamed Tavakoli
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas, 79968, USA.
| | - Elisabeth Hirth
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas, 79968, USA.
- Department of Chemistry, University of Aalen, Beethovenstraße 1, 73430 Aalen, Germany
| | - Man Luo
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas, 79968, USA.
| | - Sanjay Sharma Timilsina
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas, 79968, USA.
| | - Maowei Dou
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas, 79968, USA.
| | - Delfina C Dominguez
- College of Health Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - XiuJun Li
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas, 79968, USA.
- Border Biomedical Research Center, Biomedical Engineering, University of Texas at El Paso, El Paso, 79968, USA
- Environmental Science and Engineering, University of Texas at El Paso, El Paso, 79968, USA
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Ortiz-Cartagena C, Fernández-García L, Blasco L, Pacios O, Bleriot I, López M, Cantón R, Tomás M. Reverse Transcription-Loop-Mediated Isothermal Amplification-CRISPR-Cas13a Technology as a Promising Diagnostic Tool for SARS-CoV-2. Microbiol Spectr 2022; 10:e0239822. [PMID: 36169448 PMCID: PMC9604158 DOI: 10.1128/spectrum.02398-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/07/2022] [Indexed: 01/04/2023] Open
Abstract
At the end of 2019, a new coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), caused a pandemic that persists to date and has resulted in more than 6.2 million deaths. In the last couple of years, researchers have made great efforts to develop a diagnostic technique that maintains high levels of sensitivity and specificity, since an accurate and early diagnosis is required to minimize the prevalence of SARS-CoV-2 infection. In this context, CRISPR-Cas systems are proposed as promising tools for development as diagnostic techniques due to their high specificity, highlighting that Cas13 endonuclease discriminates single nucleotide changes and displays collateral activity against single-stranded RNA molecules. With the aim of improving the sensitivity of diagnosis, this technology is usually combined with isothermal preamplification reactions (SHERLOCK, DETECTR). Based on this, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP)-CRISPR-Cas13a method for SARS-CoV-2 virus detection in nasopharyngeal samples without using RNA extraction that exhibits 100% specificity and 83% sensitivity, as well as a positive predictive value (PPV) of 100% and negative predictive values (NPVs) of 100%, 81%, 79.1%, and 66.7% for cycle threshold (CT) values of <20, 20 to 30, >30 and overall, respectively. IMPORTANCE The coronavirus disease 2019 (COVID-19) crisis has driven the development of innovative molecular diagnosis methods, including CRISPR-Cas technology. In this work, we performed a protocol, working with RNA extraction kit-free samples and using RT-LAMP-CRISPR-Cas13a technology; our results place this method at the forefront of rapid and specific diagnostic methods for COVID-19 due to the high specificity (100%), sensitivity (83%), PPVs (100%), and NPVs (81% for high viral loads) obtained with clinical samples.
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Affiliation(s)
- Concha Ortiz-Cartagena
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Laura Fernández-García
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Lucia Blasco
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Olga Pacios
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Inés Bleriot
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María López
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - María Tomás
- Translational and Multidisciplinary Microbiology (MicroTM), Biomedical Research Institute A Coruña (INIBIC), Microbiology Department, Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Spanish Network for Research in Infectious Diseases (REIPI) and CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Paruch L. Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:5128. [PMID: 35564522 PMCID: PMC9105083 DOI: 10.3390/ijerph19095128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022]
Abstract
Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research-NIBIO Oluf Thesens vei 43, 1433 Aas, Norway
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Ghosh S, Straus DL, Good C, Phuntumart V. Development and comparison of loop-mediated isothermal amplification with quantitative PCR for the specific detection of Saprolegnia spp. PLoS One 2021; 16:e0250808. [PMID: 34898622 PMCID: PMC8668100 DOI: 10.1371/journal.pone.0250808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 11/07/2021] [Indexed: 11/26/2022] Open
Abstract
Saprolegniasis is an important disease in freshwater aquaculture, and is associated with oomycete pathogens in the genus Saprolegnia. Early detection of significant levels of Saprolegnia spp. pathogens would allow informed decisions for treatment which could significantly reduce losses. This study is the first to report the development of loop-mediated isothermal amplification (LAMP) for the detection of Saprolegnia spp. and compares it with quantitative PCR (qPCR). The developed protocols targeted the internal transcribed spacer (ITS) region of ribosomal DNA and the cytochrome C oxidase subunit 1 (CoxI) gene and was shown to be specific only to Saprolegnia genus. This LAMP method can detect as low as 10 fg of S. salmonis DNA while the qPCR method has a detection limit of 2 pg of S. salmonis DNA, indicating the superior sensitivity of LAMP compared to qPCR. When applied to detect the pathogen in water samples, both methods could detect the pathogen when only one zoospore of Saprolegnia was present. We propose LAMP as a quick (about 20–60 minutes) and sensitive molecular diagnostic tool for the detection of Saprolegnia spp. suitable for on-site applications.
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Affiliation(s)
- Satyaki Ghosh
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - David L. Straus
- United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree-Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, United States of America
| | - Christopher Good
- The Conservation Fund’s Freshwater Institute, Shepherdstown, West Virginia, United States of America
| | - Vipaporn Phuntumart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
- * E-mail:
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11
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Detection of blueberry stunt phytoplasma in Eastern Canada using cpn60-based molecular diagnostic assays. Sci Rep 2021; 11:22118. [PMID: 34764366 PMCID: PMC8586236 DOI: 10.1038/s41598-021-01439-4] [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: 06/28/2021] [Accepted: 10/25/2021] [Indexed: 11/15/2022] Open
Abstract
Blueberry stunt phytoplasma (BBSP; ‘Candidatus Phytoplasma asteris’) is an insect-vectored plant pathogen that causes severe yield losses in blueberry (Vaccinium corymbosum), which is the most valuable fruit crop in Canada. Rapid, field-based diagnostic assays are desirable tools for the control of BBSP, as part of an integrated, proactive approach to production management termed biovigilance. We designed and validated a chaperonin-60 (cpn60)-targeted LAMP assay for detection of BBSP, providing a rapid, low cost, field-deployable diagnostic option. Our validation demonstrates that the assay is reproducible, with high analytical specificity and improved sensitivity when compared with 16S rRNA nested PCR. We applied the validated LAMP assay to nearly 2000 blueberry samples from Québec and Nova Scotia over three growing seasons (2016–2018). Our surveys revealed that BBSP is present in most sites across both provinces, though detection of the pathogen in individual plants varied in different tissues across sampling dates and across years, and evidence of spread between plants was limited. To quantify pathogen load in select plants, we designed additional qPCR and ddPCR assays, also based on cpn60. We found that pathogen load fluctuates in individual plants, both within and between growing seasons. Finally, we designed an interactive map to visualize the results of our surveys. These results provide a validated diagnostic assay that can be used as part of a biovigilance strategy for detecting and controlling infections caused by BBSP.
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Jang YO, Lee HJ, Koo B, Cha HH, Kwon JS, Kim JY, Kim MG, Kim HS, Kim SH, Shin Y. Rapid COVID-19 Molecular Diagnostic System Using Virus Enrichment Platform. BIOSENSORS-BASEL 2021; 11:bios11100373. [PMID: 34677329 PMCID: PMC8534047 DOI: 10.3390/bios11100373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 12/22/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus (SARS-CoV)-2, is rapidly spreading and severely straining the capacities of public health communities and systems around the world. Therefore, accurate, rapid, and robust diagnostic tests for COVID-19 are crucial to prevent further spread of the infection, alleviate the burden on healthcare and diagnostic facilities, and ensure timely therapeutic intervention. To date, several detection methods based on nucleic acid amplification have been developed for the rapid and accurate detection of SARS-CoV-2. Despite the myriad of advancements in the detection methods for SARS-CoV-2, rapid sample preparation methods for RNA extraction from viruses have rarely been explored. Here, we report a rapid COVID-19 molecular diagnostic system that combines a self-powered sample preparation assay and loop-mediated isothermal amplification (LAMP) based naked-eye detection method for the rapid and sensitive detection of SARS-CoV-2. The self-powered sample preparation assay with a hydrophilic polyvinylidene fluoride filter and dimethyl pimelimidate can be operated by hand, without the use of any sophisticated instrumentation, similar to the reverse transcription (RT)-LAMP-based lateral flow assay for the naked-eye detection of SARS-CoV-2. The COVID-19 molecular diagnostic system enriches the virus population, extracts and amplifies the target RNA, and detects SARS-CoV-2 within 60 min. We validated the accuracy of the system by using 23 clinical nasopharyngeal specimens. We envision that this proposed system will enable simple, facile, efficient, and inexpensive diagnosis of COVID-19 at home and the clinic as a pre-screening platform to reduce the burden on the medical staff in this pandemic era.
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Affiliation(s)
- Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
| | - Hye-Hee Cha
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Ji-Soo Kwon
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
| | - Myoung Gyu Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology (AMIST), University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea
| | - Hyun Soo Kim
- INFUSIONTECH, 38, Heungan-daero 427 beon-gil, Dongan-gu, Anyang-si 14059, Korea;
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Korea; (H.-H.C.); (J.-S.K.); (J.Y.K.)
- Correspondence: (S.-H.K.); (Y.S.)
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.O.J.); (H.J.L.); (B.K.); (M.G.K.)
- Correspondence: (S.-H.K.); (Y.S.)
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13
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Chen X, Wang S, Tan Y, Huang J, Yang X, Li S. Nanoparticle-Based Lateral Flow Biosensors Integrated With Loop-Mediated Isothermal Amplification for the Rapid and Visual Diagnosis of Hepatitis B Virus in Clinical Application. Front Bioeng Biotechnol 2021; 9:731415. [PMID: 34595159 PMCID: PMC8477041 DOI: 10.3389/fbioe.2021.731415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatitis B virus (HBV) infection remains one of the major public health issues worldwide. Developing a rapid, sensitive, specific, easy-to-operate, and cost-saving approach for the diagnosis of HBV is essential for its therapy and prevention. Here, we first devised a novel approach, termed “loop-mediated isothermal amplification integrated with a nanoparticle-based lateral flow biosensor (LAMP-LFB),” for the detection of HBV in clinical application. The results indicated that a set of LAMP primers based on the S gene were valid for the establishment of HBV-LAMP-LFB. The optimal HBV-LAMP can be carried out at a constant temperature of 65°C for 40 min. The whole detection process, including HBV genomic DNA preparation (∼10 min), LAMP (40 min), and LFB reading (within 2 min), can be accomplished within 60 min. The limit of detection of the HBV-LAMP-LFB assay was 7.5 IU per test. The specificity of this assay was one hundred percent, and there was no cross-reactivity with other pathogens. Hence, these results indicated that the HBV-LAMP-LFB assay established in the current study is a sensitive, rapid, specific, visual, simple, and cost-saving method for the screening of HBV agents. More importantly, the HBV-LAMP-LFB has remarkable potential to develop a point-of-care testing in clinical application, especially in resource-scarce regions.
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Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, China.,Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Shoshi Wang
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yan Tan
- Guizhou Provincial Center for Clinical Laboratory, Guiyang, China
| | - Junfei Huang
- Laboratory of Bacterial Infectious Disease of Experimental Centre, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Xingui Yang
- Laboratory of Bacterial Infectious Disease of Experimental Centre, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
| | - Shijun Li
- Laboratory of Bacterial Infectious Disease of Experimental Centre, Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
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Assessment of a Multiplex LAMP Assay (Eazyplex ® CSF Direct M) for Rapid Molecular Diagnosis of Bacterial Meningitis: Accuracy and Pitfalls. Microorganisms 2021; 9:microorganisms9091859. [PMID: 34576754 PMCID: PMC8471247 DOI: 10.3390/microorganisms9091859] [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: 07/20/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 11/23/2022] Open
Abstract
Background: Automated molecular panels are attractive tools for improving early meningitis diagnosis. This study assessed the Eazyplex® CSF direct M panel (EP), a multiplex real-time Loop-Mediated Isothermal Amplification assay. Methods: From December 2016 to December 2019, cerebrospinal fluid (CSF) samples were routinely tested with the EP V1.0. CSF parameters and microbiological and clinical data were retrospectively collected. Results: Out of 230 CSF samples, the EP yielded positive, negative, and invalid results for 32 (13.9%) (16 N. meningitidis, nine S. pneumoniae, two S. agalactiae, two E. coli, two H. influenzae, one L. monocytogenes), 182 (79.1%), and 16 (7%) samples, respectively. Among the positive samples, 14 (44%) remained negative in culture (antibiotic therapy before lumbar puncture (n = 11), meningococcal meningitis (n = 3)). High CSF protein concentrations and cellularity were associated with LAMP inhibition, counteracted by centrifugation. The automated software yielded 13 false positive and five false negative results. Amplification curve analysis was necessary and enabled the attainment of positive (PPA) and negative percentage agreement and positive and negative predictive values of 91.4%, 100%, 100%, and 98.3%. Three false negative results remained (two E. coli and one N. meningitidis). E. coli presented the poorest PPA (50%). Conclusion: This work confirms the strong performance of the EP, of particular interest in cases of antibiotic therapy before lumbar puncture.
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Ikken Y, Benaouda A, Yaich LI, Hilali F, Sekhsokh Y, Charof R. Simultaneous detection of Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae by quantitative PCR from CSF samples with negative culture in Morocco. Acta Microbiol Immunol Hung 2021; 68:107-112. [PMID: 33512333 DOI: 10.1556/030.2021.01344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/09/2021] [Indexed: 11/19/2022]
Abstract
Bacteriological cultures from cerebrospinal fluids (CSF) have less sensitivity and specificity compared to quantitative PCR (RT-PCR), and multiple facts still conduct to the increase of negative culture. The aims of this study are to determine the molecular epidemiology and the simultaneous detection of bacterial meningitis in Morocco by using RT-PCR and compared this molecular approach with culture method to improve the etiological diagnosis of meningitis. The CSFs were collected over one-year period in 2018 in different hospitals covering all regions of the Kingdom of Morocco, from patients with suspected meningitis. The results showed the confirmation rate per culture recorded a rate of 33% and the RT-PCR of 70%. Molecular epidemiology is predominant of Neisseria meningitidis followed by Streptococcus pneumoniae and a dramatic reduction in meningitis due to Haemophilus influenzae following the introduction of conjugate vaccine in 2007. Also, the epidemiological profile shows a sex ratio M/F of 1.4 and a median age of 2 years. The national distribution showed a predominant of meningococcal disease followed by pneumococcal disease, especially a dominance of N. meningitidis over S. pneumoniae in two regions and a slight predominance of S. pneumoniae in the other two regions over N. meningitidis. Our research shows that culture in our country has less sensitivity and specificity than RT-PCR in diagnosis of bacterial meningitis and that molecular biology technique at bacteriology laboratories is desirable for diagnosis, early management of meningitis cases and in the context of the surveillance of meningitis in Morocco in parallel with culture.
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Affiliation(s)
- Youssef Ikken
- 1Biosafety Level 3 and Research Laboratory, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat 10 000, Morocco
- 2Laboratory of Medical Bacteriology, National Institute of Hygiene in Rabat, 27, Avenue Ibn Batouta, B.P. 769, Rabat 10 000, Morocco
| | - Amina Benaouda
- 3Laboratory of Microbiology, Cheick-Zaid University Hospital, University Internationale Abulcasis of Sciences and Health in Rabat, B.P. 6533, Avenue Allal El Fassi, Madinat Al Irfane, Rabat 10 000, Morocco
| | - Latifa Ibn Yaich
- 4Regional laboratory of Medical Bacteriology, Mohamed V Hospital in Tangier. 1 Avenue Moulay Rachid, Tangier 90100, Morocco
| | - Farida Hilali
- 1Biosafety Level 3 and Research Laboratory, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat 10 000, Morocco
| | - Yassine Sekhsokh
- 1Biosafety Level 3 and Research Laboratory, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat 10 000, Morocco
| | - Réda Charof
- 2Laboratory of Medical Bacteriology, National Institute of Hygiene in Rabat, 27, Avenue Ibn Batouta, B.P. 769, Rabat 10 000, Morocco
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16
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Wong Tzeling JM, Engku Nur Syafirah EAR, Irekeola AA, Yusof W, Aminuddin Baki NN, Zueter A, Harun A, Chan YY. One-step, multiplex, dual-function oligonucleotide of loop-mediated isothermal amplification assay for the detection of pathogenic Burkholderia pseudomallei. Anal Chim Acta 2021; 1171:338682. [PMID: 34112436 DOI: 10.1016/j.aca.2021.338682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/18/2022]
Abstract
This study highlights the development of a multiplex real-time loop-mediated isothermal amplification assay. The developed assay employed a dual-function oligonucleotide (DFO) which simultaneously monitors the emitted amplification signals and accelerates the amplification process. The DFO was a modification of loop primer (LP); the 5'-end and 3'-end of the LP was tagged with fluorophore and quencher, respectively. The DFO was quenched in its unbound state and fluoresces only when it anneals to the specific target during the amplification process. With the same working mechanism as LP, DFO allowed the detection of target genes in less than 1 h in a real time monitoring system. We demonstrated this detection platform with Burkholderia pseudomallei, the causative agent of melioidosis. An internal amplification control (IAC) was incorporated in the assay to rule out false negative result and to demonstrate that the assay was successfully developed in a multiplex system. The assay was 100% specific when it was evaluated against 96 B. pseudomallei clinical isolates and 48 other bacteria species. The detection limit (sensitivity) of the developed assay was 1 fg/μl of B. pseudomallei genomic DNA and 18.2 CFU/ml at the bacterial cell level. In spiked blood samples, the assay's detection limit was 14 CFU/ml. The assay's diagnostic evaluation showed 100% diagnostic sensitivity, diagnostic specificity, positive predictive value, and negative predictive value. An integrated multiplex LAMP and real-time monitoring system was successfully developed, simplifying the workflow for the rapid and specific nucleic acid diagnostic test.
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Affiliation(s)
- Jilien Michelle Wong Tzeling
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - E A R Engku Nur Syafirah
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, PMB 4412, Offa Kwara State, Nigeria.
| | - Wardah Yusof
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Nurul Najian Aminuddin Baki
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - AbdelRahman Zueter
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Department of Medical Laboratory Sciences, Faculty of Applied Health Sciences, The Hashemite University, 13133, Zarqa, Jordan.
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Yean Yean Chan
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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Development of a Loop-mediated isothermal amplification (LAMP) technique for specific and early detection of Mycobacterium leprae in clinical samples. Sci Rep 2021; 11:9859. [PMID: 33972644 PMCID: PMC8110778 DOI: 10.1038/s41598-021-89304-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/19/2021] [Indexed: 11/26/2022] Open
Abstract
Leprosy, a progressive, mutilating and highly stigmatized disease caused by Mycobacterium leprae (ML), continues to prevail in the developing world. This is due to the absence of rapid, specific and sensitive diagnostic tools for its early detection since the disease gets notified only with the advent of physical scarring in patients. This study reports the development of a Loop-mediated isothermal amplification (LAMP) technique for fast, sensitive and specific amplification of 16S rRNA gene of ML DNA for early detection of leprosy in resource-limited areas. Various parameters were optimized to obtain robust and reliable amplification of ML DNA. Blind clinical validation studies were performed which showed that this technique had complete concurrence with conventional techniques. Total absence of amplification of negative control DNA confirmed the specificity of this test. Various visual detection methods viz. colorimetric, turbidity differentiation and bridge flocculation were standardized to establish easy-to-read and rapid diagnosis. This technique eliminates the lack of accuracy and sensitivity in skin smear tests in patients and the requirement for expensive lab equipments and trained technicians. The technique holds promise for further expansion and has the potential to cater to the unmet needs of society for a cheap, highly-sensitive and robust rapid diagnosis of ML.
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18
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An improved primer design for the loop-mediated isothermal amplification (LAMP) method to detect oxacillinase (OXA)-48 β-lactamase genes in Gram-negative bacteria for clinical applications. J Infect Chemother 2021; 27:1005-1012. [PMID: 33814349 DOI: 10.1016/j.jiac.2021.02.016] [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: 06/18/2020] [Revised: 02/07/2021] [Accepted: 02/13/2021] [Indexed: 11/21/2022]
Abstract
INTRODUCTION Recently, increased frequencies of carbapenemase-producing Enterobacteriaceae have been reported worldwide. Among multiple genetic subtypes, oxacillinase (OXA)-48 β-lactamase-producing strains have been associated with inbound infection because they have been detected predominantly in patients who traveled outside of Japan. However, a recent case report of OXA-48 β-lactamase-producing Enterobacteriaceae suggested the latent spread of domestic infections. Due to a lack of specific inhibitors, culture-based detection of OXA-48 β-lactamase-producing bacteria is difficult. Thus, DNA-based detection methods, including PCR, direct sequencing and loop-mediated isothermal amplification (LAMP), have been employed. Among these methods, LAMP detection is more favorable than other methods because of its technical simplicity and low cost. METHODS We designed novel LAMP primers to detect OXA-48 β-lactamase-producing bacteria and investigated their possible clinical applications with bacterial genome-spiked human materials (cerebrospinal fluid, blood, feces, urine, and sputum). We evaluated the specificity of the LAMP primers using 37 bacterial strains: 8 standard, 9 reference, and 20 clinical Gram-negative strains. RESULTS Our LAMP primers detected 10 copies of the OXA-48 type β-lactamase gene and exhibited no cross reactivity with other β-lactamase genes. Sensitivity was not influenced in any clinical sample, in contrast to PCR detection, which was strongly inhibited by substances in fecal samples. CONCLUSIONS These results suggest the superior performance of LAMP compared with conventional PCR for detecting the OXA-48 type β-lactamase gene in various clinical samples.
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Garcia-Venzor A, Rueda-Zarazua B, Marquez-Garcia E, Maldonado V, Moncada-Morales A, Olivera H, Lopez I, Zuñiga J, Melendez-Zajgla J. SARS-CoV-2 Direct Detection Without RNA Isolation With Loop-Mediated Isothermal Amplification (LAMP) and CRISPR-Cas12. Front Med (Lausanne) 2021; 8:627679. [PMID: 33681254 PMCID: PMC7928313 DOI: 10.3389/fmed.2021.627679] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/25/2021] [Indexed: 11/16/2022] Open
Abstract
As to date, more than 49 million confirmed cases of Coronavirus Disease 19 (COVID-19) have been reported worldwide. Current diagnostic protocols use qRT-PCR for viral RNA detection, which is expensive and requires sophisticated equipment, trained personnel and previous RNA extraction. For this reason, we need a faster, direct and more versatile detection method for better epidemiological management of the COVID-19 outbreak. In this work, we propose a direct method without RNA extraction, based on the Loop-mediated isothermal amplification (LAMP) and Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated protein (CRISPR-Cas12) technique that allows the fast detection of SARS-CoV-2 from patient samples with high sensitivity and specificity. We obtained a limit of detection of 16 copies/μL with high specificity and at an affordable cost. The diagnostic test readout can be done with a real-time PCR thermocycler or with the naked eye in a blue-light transilluminator. Our method has been evaluated on a small set of clinical samples with promising results.
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Affiliation(s)
- Alfredo Garcia-Venzor
- Cancer Functional Genomics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Bertha Rueda-Zarazua
- Cancer Functional Genomics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Eduardo Marquez-Garcia
- Molecular Biology Unit, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Vilma Maldonado
- Epigenetics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - Hiram Olivera
- Instituto Nacional de Referencia Epidemiológica, Mexico City, Mexico
| | - Irma Lopez
- Instituto Nacional de Referencia Epidemiológica, Mexico City, Mexico
| | - Joaquin Zuñiga
- Molecular Biology Unit, Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Jorge Melendez-Zajgla
- Cancer Functional Genomics Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
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Lee J, Yoon Y, Kim EJ, Lee D, Baek Y, Takano C, Chang B, Iijima T, Kilgore PE, Hayakawa S, Hoshino T, Kim DW, Seki M. 23-valent polysaccharide vaccine (PPSV23)-targeted serotype-specific identification of Streptococcus pneumoniae using the loop-mediated isothermal amplification (LAMP) method. PLoS One 2021; 16:e0246699. [PMID: 33591996 PMCID: PMC7886117 DOI: 10.1371/journal.pone.0246699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/22/2021] [Indexed: 11/21/2022] Open
Abstract
Reports of invasive disease due to Streptococcus pneumoniae have declined since the introduction of pneumococcal conjugate vaccines (PCV7 and PCV13). The incidence of invasive diseases due to S. pneumoniae that are not addressed by the vaccines, however, has increased in children and adults, creating a global public health problem. Previously, we established the loop-mediated isothermal amplification (LAMP) method for a PCV13 serotype-specific assay. In the current study, we developed a rapid, simple, and cost-effective assay to detect serotypes in the 23-valent pneumococcal polysaccharide vaccine (PPSV23) using the LAMP method. In this study, LAMP primer sets for serotypes 2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20, 22F, and 33F of S. pneumoniae were developed. The reactivity, specificity, and sensitivity of LAMP assays were determined and compared to those of conventional PCR. The feasibility of LAMP assays in clinical application in patients with invasive pneumococcal diseases was validated by defining the detection limit of the LAMP assay with bacterial genomic DNA-spiked blood specimens. The specificity of each LAMP assay was determined using 44 serotypes of pneumococcal strains. Their sensitivity was 100 copies per reaction versus 103 to 106 copies per reaction for PCR assays. Using DNA-spiked blood specimens, excluding the LAMP assay that targeted serotype 22F (103 copies per reaction), the limit of detection of the LAMP assay was similar to that with purified DNA as the template (102 copies per reaction), compared with 103 to >106 copies per reaction for PCR assays. In conclusion, a rapid and simple LAMP-based PPSV23-targeted serotype detection assay was developed for use in many countries. This study is the first report of a LAMP-based assay for identification of PPSV23 serotypes. Further evaluation of this assay is needed through surveillance and vaccine efficacy studies.
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Affiliation(s)
- Jiwon Lee
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Youngbae Yoon
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Eun Jin Kim
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Donghyun Lee
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Yeongjun Baek
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Bin Chang
- Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takahiro Iijima
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | - Paul E. Kilgore
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, United States of America
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea
- Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Mitsuko Seki
- Division of Pediatric Dentistry, Department of Human Development and Fostering, Meikai University School of Dentistry, Saitama, Japan
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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Lyu M, Cheng Y, Zhou J, Chong W, Wang Y, Xu W, Ying B. Systematic evaluation, verification and comparison of tuberculosis-related non-coding RNA diagnostic panels. J Cell Mol Med 2020; 25:184-202. [PMID: 33314695 PMCID: PMC7810967 DOI: 10.1111/jcmm.15903] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/23/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
We systematically summarized tuberculosis (TB)‐related non‐coding RNA (ncRNA) diagnostic panels, validated and compared panel performance. We searched TB‐related ncRNA panels in PubMed, OVID and Web of Science up to 28 February 2020, and available datasets in GEO, SRA and EBI ArrayExpress up to 1 March 2020. We rebuilt models and synthesized the results of each model in validation sets by bivariate mixed models. Specificity at 90% sensitivity, area under curve (AUC) and inconsistence index (I2) were calculated. NcRNA biofunctions were analysed. Nineteen models based on 18 ncRNA panels (miRNA, lncRNA, circRNA and snoRNA panels) and 18 datasets were included. Limited available datasets only allowed to evaluate miRNA panels further. Cui 2017 and Latorre 2015 exhibited specificity >70% at 90% sensitivity and AUC >80% in all validation sets. Cui 2017 showed higher specificity at 90% sensitivity (92%) and AUC (95%) and lower heterogeneity (I2 = 0%) in ethological‐confirmation validation sets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that most ncRNAs in panels involved in immune cell activation, oxidative stress, and Wnt and MAPK signalling pathway. Cui 2017 outperformed other models in both all available and aetiological‐confirmed validation sets, meeting the criteria of target product profile of WHO. This work provided a basis for clinical choice of TB‐related ncRNA diagnostic panels to a certain extent.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Yuhui Cheng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Jian Zhou
- West China School of Medicine, Sichuan University, Chengdu, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Weelic Chong
- Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,West China School of Medicine, Sichuan University, Chengdu, China
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22
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Ahlawat S, Chaudhary R, Dangi M, Bala K, Singh M, Chhillar AK. Advances in tuberculous meningitis diagnosis. Expert Rev Mol Diagn 2020; 20:1229-1241. [PMID: 33259249 DOI: 10.1080/14737159.2020.1858805] [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: 10/22/2022]
Abstract
Introduction: Tuberculous meningitis (TBM) is the most devastating form of central nervous system tuberculosis (TB) and causes high mortality worldwide. Nonspecific clinical manifestations and limited sensitivity of existing laboratory methods make the diagnosis elusive due to the paucibacillary nature of the infection. Areas Covered: We reviewed current literature on the adequacy and limitations of globally existing laboratory methods for diagnosing TBM. Expert opinion: TBM is deadliest among all TB forms, as the outcome may lead to death in 50% of cases, and survivors undergo irreversible neurological disorders. Therefore, early diagnosis and prompt treatment are cornerstones of effective disease management. Conventional microscopy and culture are widely used modalities but remain inadequate in most TBM cases. Although expanded use of rapid molecular tests such as real-time PCR and Xpert Ultra, even in resource-limited settings, hold promising results for TB diagnosis but need optimization for early detection of TBM. Moreover, CSF IGRA is also used but unable to differentiate between active and latent TB. Overall no single test for diagnosing TBM has adequate accuracy so, there is an urgent need to devise a point-of-care test.
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Affiliation(s)
- Sonia Ahlawat
- Centre for Biotechnology, Maharshi Dayanand University (MDU) , Rohtak, India.,Amity Institute of Biotechnology, Amity University Haryana , Manesar, India
| | - Renu Chaudhary
- Council of Scientific & Industrial Research (CSIR)-institute of Genomics and Integrative Biology (IGIB) , New Delhi, India
| | - Mehak Dangi
- Department of Bioinformatics, Maharshi Dayanand University (MDU) , Rohtak, India
| | - Kiran Bala
- Department of Neurology, University of Health Sciences (UHS) , Rohtak, India
| | - Machiavelli Singh
- Amity Institute of Biotechnology, Amity University Haryana , Manesar, India
| | - Anil Kumar Chhillar
- Centre for Biotechnology, Maharshi Dayanand University (MDU) , Rohtak, India
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23
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Loop-mediated Isothermal Amplification (LAMP) for Identification of Pythium insidiosum. Int J Infect Dis 2020; 101:149-159. [PMID: 32987181 DOI: 10.1016/j.ijid.2020.09.1430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Pythium insidiosum causes a life-threatening condition called pythiosis. High morbidity and mortality of pythiosis are consequences of delayed diagnosis. We aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of P. insidiosum for use in remote areas, where pythiosis is prevalent. METHODS We designed four LAMP primers to amplify the rDNA sequence. A side-by-side comparison evaluated performances of LAMP and the previously-established multiplex PCR (M-PCR), using gDNA samples extracted from colonies of P. insidiosum (n = 28) and other fungi (n = 54), and tissues of animals with (n = 16) or without (n = 13) pythiosis. RESULTS LAMP demonstrated a 50% shorter assay duration (1.5 h) and a 10-fold lower limit of detection (10-4 ng) than did M-PCR. Based on colony-extracted gDNAs, LAMP and M-PCR correctly reported P. insidiosum in all 28 samples, providing 100% sensitivity. While M-PCR did not amplify all fungal controls (100% specificity), LAMP falsely detected one organism (98% specificity). Based on the clinical samples, LAMP and M-PCR provided an equivalently-high specificity (100%). However, LAMP showed a markedly-higher sensitivity than that of M-PCR (88% vs. 56%). CONCLUSIONS LAMP is a simple, useful, efficient assay for the detection of P. insidiosum in clinical specimens and pure cultures in resource-limited laboratories.
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24
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Next generation rapid diagnostic tests for meningitis diagnosis. J Infect 2020; 81:712-718. [PMID: 32888978 DOI: 10.1016/j.jinf.2020.08.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 02/01/2023]
Abstract
Rapid diagnostic tests (RDTs) are increasingly recognized as valuable, transformative tools for the diagnosis of infectious diseases. Although there are a variety of meningitis RDTs currently available, certain product features restrict their use to specific levels of care and settings. For this reason, the development of meningitis RDTs for use at all levels of care, including those in low-resource settings, was included in the "Defeating Meningitis by 2030" roadmap. Here we address the limitations of available meningitis RDTs and present test options and specifications to consider when developing the next generation of meningitis RDTs.
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25
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Fan SJ, Tan HK, Xu YC, Chen YZ, Xie TA, Pan ZY, Ouyang S, Li Q, Li XY, Li ZX, Guo XG. A pooled analysis of the LAMP assay for the detection of Neisseria meningitidis. BMC Infect Dis 2020; 20:525. [PMID: 32689953 PMCID: PMC7372874 DOI: 10.1186/s12879-020-05250-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 07/14/2020] [Indexed: 12/13/2022] Open
Abstract
Background Neisseria meningitidis is a major cause of bacterial meningitis, and these infections are associated with a high mortality rate. Rapid and reliable diagnosis of bacterial meningitis is critical in clinical practice. However, this disease often occurs in economically depressed areas, so an inexpensive, easy to use, and accurate technology is needed. We performed a pooled-analysis to assess the potential of the recently developed loop-mediated isothermal amplification (LAMP) assay for detection of meningococcus. Methods Pubmed, Embase, and Web of Science were searched to identify original studies that used the LAMP assay to detect meningococcus. After pooling of data, the sensitivity and specificity were calculated, a summary receiver operating characteristic (SROC) curve was determined, and the area under the SROC curve was computed to determine diagnostic accuracy. Publication bias was assessed using Deek’s funnel plot. Results We examined 14 studies within 6 publications. The LAMP assay had high sensitivity (94%) and specificity (100%) in the detection of meningococcus in all studies. The area under the SROC curve (0.980) indicated high overall accuracy of the LAMP assay. There was no evidence of publication bias. Discussion The LAMP assay has accuracy comparable to bacterial culture and PCR for detection of meningococcus, but is less expensive and easier to use. We suggest the adoption of the LAMP assay to detect meningococcus, especially in economically depressed areas.
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Affiliation(s)
- Shu-Jin Fan
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Hong-Kun Tan
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Yu-Cheng Xu
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Yuan-Zhi Chen
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Tian-Ao Xie
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Zhi-Yong Pan
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Shi Ouyang
- Department of infectious disease, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qin Li
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, USA
| | - Xiao-Yan Li
- Department of Laboratory Medicine, The Affiliated Shunde Hospital of Guangzhou Medical University, Foshan, China
| | - Zhen-Xing Li
- Department of respiratory, The third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Department of Clinical Medicine, the Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China. .,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, 510150, China. .,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, 510150, China.
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26
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Chen X, Ma K, Yi X, Xiong L, Wang Y, Li S. The rapid and visual detection of methicillin-susceptible and methicillin-resistant Staphylococcus aureus using multiplex loop-mediated isothermal amplification linked to a nanoparticle-based lateral flow biosensor. Antimicrob Resist Infect Control 2020; 9:111. [PMID: 32680560 PMCID: PMC7366892 DOI: 10.1186/s13756-020-00774-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/09/2020] [Indexed: 12/16/2022] Open
Abstract
Background Staphylococcus aureus (S. aureus), including methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA), is an eminent human pathogen that can colonize the human host and cause severe life-threatening infections. The development of a reliable, simple and rapid assay for detecting S. aureus and identifying MRSA is important for diagnosis and follow-up treatment. Methods A novel molecular diagnosis technique, named multiplex loop-mediated isothermal amplification linked to a nanoparticle-based lateral flow biosensor (m-LAMP-LFB), was applied to detect all S. aureus species and identify MRSA. Two sets of primers were designed based on the femA gene (S. aureus-specific gene) and the mecA gene (encoding penicillin-binding protein 2a), and the multiple-LAMP products were analyzed using LFB. The m-LAMP-LFB amplification conditions, including the target DNA concentration, reaction temperature and time, were optimized. The sensitivity and specificity of the m-LAMP-LFB method were tested in the current study, and the multiple-LAMP-LFB technology was applied to detect the MSSA and MRSA strains from clinical samples. Results The S. aureus- and MRSA-specific primers based on the femA and mecA genes allowed the multiple-LAMP technology to detect S. aureus and MRSA, respectively. The multiple-LAMP conditions were optimized at 63 °C for 40 min. The full process, including genomic DNA template preparation, LAMP, and product identification, could be achieved in 80 min. The limit of detection (LoD) of the multiple-LAMP assay for femA and mecA detection was 100 fg of genomic DNA template per reaction. The specificity of m-LAMP-LFB detection was 100 %, and no cross-reactions to non-S. aureus strains were observed. Conclusion The multiple-LAMP-LFB technique developed in the current study is a reliable, simple, rapid, specific and sensitive method to identify MSSA and MRSA infections for appropriate antibiotic therapy.
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Affiliation(s)
- Xu Chen
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China.,The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China.,Laboratory of Bacterial Infectious Disease of Experimental Center, Guizhou Provincial Centre for Disease Control and Prevention, 73 Bageyan Road, Guiyang, Guizhou, 550004, P.R. China
| | - Kai Ma
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China
| | - Xu Yi
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China
| | - Lijuan Xiong
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550003, P.R. China
| | - Yu Wang
- Department of Clinical Laboratory Centre, The First People's Hospital of Guiyang, Guiyang, Guizhou, 55004, P.R. China
| | - Shijun Li
- Laboratory of Bacterial Infectious Disease of Experimental Center, Guizhou Provincial Centre for Disease Control and Prevention, 73 Bageyan Road, Guiyang, Guizhou, 550004, P.R. China.
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Lázaro-Rodríguez P, López-Gijón J, Alonso S, Herrera-Viedma E. Actualidad en estudios LibQUAL+®: paradigmas de la biblioteca informativa y social-creadora y cuestión de género como reflejos de la realidad social. REVISTA ESPANOLA DE DOCUMENTACION CIENTIFICA 2020. [DOI: 10.3989/redc.2020.2.1649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Los objetivos de este artículo son cuatro: analizar las principales diferencias en torno a las dimensiones mejor valoradas de tres estudios sobre satisfacción de personas usuarias basados en LibQUAL+® llevados a cabo en bibliotecas universitarias de España, Argentina y Chile; analizar las diferencias atendiendo a la variable de género (hombres y mujeres); determinar si las diferencias en cuanto a género son estadísticamente significativas; y discutir y reflexionar sobre los resultados hallados en el ámbito concreto de las bibliotecas como reflejo de la realidad social en general. Los resultados permiten concluir que en España las personas usuarias están menos satisfechas con la dimensión de la biblioteca como espacio, mientras que en Latinoamericana se percibe menor grado de satisfacción también con el control de la información. El mayor grado de satisfacción en todos los estudios se da en el valor afectivo del servicio. Las mujeres en España muestran menor satisfacción y mayor exigencia que los hombres en el valor afectivo del servicio. Además, se hallaron diferencias estadísticamente significativas en el análisis de las medias por género. En la discusión se ponen en relación los resultados hallados con la literatura existente, definiendo los paradigmas posibles de la biblioteca informativa frente al de la social-creadora y la percepción de la satisfacción por géneros según el contexto social en que se hallan las bibliotecas. La limitación principal del artículo es que se basa en tres estudios concretos; y su principal valor y originalidad, que puede considerarse como punto de partida para futuras investigaciones sobre la cuestión de género en lo que a bibliotecas y los servicios que ofrecen se refiere.
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Loop Mediated Isothermal Amplification: A Promising Tool for Screening Genetic Mutations. Mol Diagn Ther 2020; 23:723-733. [PMID: 31396882 DOI: 10.1007/s40291-019-00422-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutation screening is elemental for clinical diagnosis and in determining therapeutic strategies. Nucleic acid-based techniques are considered to be the most accurate tools in genetic diagnosis. One such technique is loop-mediated isothermal amplification (LAMP) assay, which has seen tremendous applications in recent years. The advantages of the assay lie in its rapidity, efficiency, sensitivity, and cost. It works in isothermal conditions and amplifies the target gene using DNA polymerases that have strand displacement activity. To date, the assay has been widely used in different fields of research, including pathogen detection, crop development, and disease diagnosis. However, despite the potential, its application in mutation screening has been minimal. This review highlights the LAMP assay and its variants that have been developed for screening single-nucleotide polymorphisms and gene translocations in cancer.
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Abstract
Infectious meningitis can be caused by viral, bacterial or fungal pathogens. Despite widely available treatments, many types of infectious meningitis are still associated with significant morbidity and mortality. Delay in diagnosis contributes to poor outcomes. Cerebrospinal fluid cultures have been used traditionally but are time intensive and sensitivity is decreased by empiric treatment prior to culture. More rapid techniques such as the cryptococcal lateral flow assay (IMMY), GeneXpert MTB/Rif Ultra (Cepheid) and FilmArray multiplex-PCR (Biofire) are three examples that have drastically changed meningitis diagnostics. This review will discuss a holistic approach to diagnosing bacterial, mycobacterial, viral and fungal meningitis.
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Affiliation(s)
- Victoria Poplin
- Department of Medicine, University of Kansas, Kansas City, KS 66160, USA
| | - David R Boulware
- Division of Infectious Diseases & International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nathan C Bahr
- Division of Infectious Diseases, Department of Medicine, University of Kansas, Kansas City, KS 66160, USA
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30
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Validation of a New Rapid Detection Test for Detection of Neisseria meningitidis A/C/W/X/Y Antigens in Cerebrospinal Fluid. J Clin Microbiol 2020; 58:JCM.01699-19. [PMID: 31915288 DOI: 10.1128/jcm.01699-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/02/2020] [Indexed: 11/20/2022] Open
Abstract
Meningococcal meningitis remains a life-threatening disease worldwide, with high prevalence in the sub-Saharan meningitis belt. A rapid diagnosis is crucial for implementing adapted antimicrobial treatment. We describe the performances of a new immunochromatographic test (MeningoSpeed, BioSpeedia, France) for detecting and grouping Neisseria meningitidis Cerebrospinal fluids (CSFs) were collected from 5 African countries and France. For the rapid diagnostic test (RDT), the CSF sample was deposited on each of the 3 cassettes for a total volume of 90 μl. The results of the RDT were compared to those of a reference multiplex PCR assay detecting the major serogroups of N. meningitidis on 560 CSF specimens. Five specimens were found uninterpretable by RDT (0.9%). The results of interpretable specimens were as follows: 305 positive and 212 negative samples by both techniques, 14 positive by PCR only, and 24 positive by RDT only (sensitivity, specificity, and positive and negative predictive values of 92.7%, 93.8%, 95.6%, and 89.8%, respectively, with an accuracy of 93.2% and a kappa test of 0.89; P < 0.05). From 319 samples positive by PCR for serogroups A, C, W, X, or Y, the grouping results were concordant for 299 specimens (sensitivity of 93.0%, 74.4%, 98.1%, 100%, and 83.3% for serogroups A, C, W, X, and Y, respectively). The MeningoSpeed RDT exhibited excellent performances for the rapid detection of N. meningitidis antigens. It can be stored at room temperature, requires a minimal amount of CSF, is performed in 15 minutes or less, and is easy to use at bedside.
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31
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Winkworth RC, Nelson BCW, Bellgard SE, Probst CM, McLenachan PA, Lockhart PJ. A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida. PLoS One 2020; 15:e0224007. [PMID: 31978166 PMCID: PMC6980612 DOI: 10.1371/journal.pone.0224007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
The root rot causing oomycete, Phytophthora agathidicida, threatens the long-term survival of the iconic New Zealand kauri. Currently, testing for this pathogen involves an extended soil bioassay that takes 14–20 days and requires specialised staff, consumables, and infrastructure. Here we describe a loop-mediated isothermal amplification (LAMP) assay for the detection of P. agathidicida that targets a portion of the mitochondrial apocytochrome b coding sequence. This assay has high specificity and sensitivity; it did not cross react with a range of other Phytophthora isolates and detected as little as 1 fg of total P. agathidicida DNA or 116 copies of the target locus. Assay performance was further investigated by testing plant tissue baits from flooded soil samples using both the extended soil bioassay and LAMP testing of DNA extracted from baits. In these comparisons, P. agathidicida was detected more frequently using the LAMP test. In addition to greater sensitivity, by removing the need for culturing, the hybrid baiting plus LAMP approach is more cost effective than the extended soil bioassay and, importantly, does not require a centralised laboratory facility with specialised staff, consumables, and equipment. Such testing will allow us to address outstanding questions about P. agathidicida. For example, the hybrid approach could enable monitoring of the pathogen beyond areas with visible disease symptoms, allow direct evaluation of rates and patterns of spread, and allow the effectiveness of disease control to be evaluated. The hybrid LAMP bioassay also has the potential to empower local communities to evaluate the pathogen status of local kauri stands, providing information for disease management and conservation initiatives.
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Affiliation(s)
- Richard C. Winkworth
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- * E-mail:
| | - Briana C. W. Nelson
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | | | | | - Peter J. Lockhart
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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32
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Takano C, Kuramochi Y, Seki M, Kim DW, Omagari D, Sasano M, Chang B, Ohnishi M, Kim EJ, Fuwa K, Kilgore PE, Hoshino T, Hayakawa S. Molecular serotype-specific identification of Streptococcus pneumoniae using loop-mediated isothermal amplification. Sci Rep 2019; 9:19823. [PMID: 31882619 PMCID: PMC6934563 DOI: 10.1038/s41598-019-56225-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/09/2019] [Indexed: 11/14/2022] Open
Abstract
In children, the incidence of pneumococcal meningitis has decreased since the introduction of pneumococcal conjugate vaccine (PCV7 and PCV13). However, since the introduction of the vaccine, developed countries have seen the emergence of non-PCV13 serotypes. However, invasive pneumococcal disease (IPD) caused by PCV13-targeted serotypes still represents an important public health problem in resource-limited countries. To develop a rapid, simple, and cost-effective assay to detect serotypes of Streptococcus pneumoniae, we developed a novel loop-mediated isothermal amplification (LAMP) assay based on the sequences available for the 13 capsular types that are included in PCV13: 1, 3, 4, 5, 6 A, 6B, 7 F, 9 V, 14, 18 C, 19 A, 19 F, and 23 F. We evaluated test reactivity, specificity, sensitivity and performance, and compared the results between established LAMP and conventional PCR assays. To support its clinical use, the detection limits of the LAMP assay were evaluated using bacterial genomic DNA-spiked cerebrospinal fluid (CSF) and blood specimens. We confirmed the specificity of the LAMP assay using 41 serotypes of pneumococcal strains. The sensitivity of the LAMP assay was 10 to 100 copies per reaction, compared to 10 to 104 copies per reaction for PCR assays. The detection limits of the LAMP assay were comparable when using DNA-spiked CSF and blood specimens, as compared to using purified DNA as the template. In conclusion, a rapid and simple LAMP-based pneumococcal serotyping method has been developed. This is the first report of a LAMP method for a PCV13 serotype-specific identification assay, which could be a promising step to facilitate epidemiological studies of pneumococcal serotyping.
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Affiliation(s)
- Chika Takano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Yoko Kuramochi
- Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Mitsuko Seki
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan. .,Department of Pediatric Dentistry, School of Dentistry, Meikai University, Saitama, Japan.
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, 15588, Republic of Korea. .,Institute of Pharmacological Research, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Daisuke Omagari
- Nihon University School of Dentistry, Tokyo, 101-8310, Japan
| | - Mari Sasano
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan.,Department of Neurological Surgery, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Bin Chang
- Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Makoto Ohnishi
- Bacteriology I, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Eun Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, 15588, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, 15588, Republic of Korea
| | - Kazumasa Fuwa
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Paul E Kilgore
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy & Health Sciences, Wayne State University, Detroit, MI, 48201, USA
| | - Tomonori Hoshino
- Department of Pediatric Dentistry, School of Dentistry, Meikai University, Saitama, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, 173-8610, Japan
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Development and Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Detection of Pistachio (Pistacia vera) in Food Samples. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01684-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Quyen TL, Ngo TA, Bang DD, Madsen M, Wolff A. Classification of Multiple DNA Dyes Based on Inhibition Effects on Real-Time Loop-Mediated Isothermal Amplification (LAMP): Prospect for Point of Care Setting. Front Microbiol 2019; 10:2234. [PMID: 31681184 PMCID: PMC6803449 DOI: 10.3389/fmicb.2019.02234] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
LAMP has received great interest and is widely utilized in life sciences for nucleic acid analysis. To monitor a real-time LAMP assay, a fluorescence DNA dye is an indispensable component and therefore the selection of a suitable dye for real-time LAMP is a need. To aid this selection, we investigated the inhibition effects of twenty-three DNA dyes on real-time LAMP. Threshold time (Tt) values of each real-time LAMP were determined and used as an indicator of the inhibition effect. Based on the inhibition effects, the dyes were classified into four groups: (1) non-inhibition effect, (2) medium inhibition effect, (3) high inhibition effect, and (4) very high inhibition effect. The signal to noise ratio (SNR) and the limit of detection (LOD) of the dyes in groups 1, 2, and 3 were further investigated, and possible inhibition mechanisms of the DNA dyes on the real-time LAMP are suggested and discussed. Furthermore, a comparison of SYTO 9 in different LAMP reactions and different systems is presented. Of the 23 dyes tested, SYTO 9, SYTO 82, SYTO 16, SYTO 13, and Miami Yellow were the best dyes with no inhibitory effect, low LOD and high SNR in the real-time LAMP reactions. The present classification of the dyes will simplify the selection of fluorescence dye for real-time LAMP assays in point of care setting.
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Affiliation(s)
- Than Linh Quyen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Tien Anh Ngo
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), National Food Institute, Technical University of Denmark (DTU-Food), Lyngby, Denmark
| | - Mogens Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Anders Wolff
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
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Ellis J, Luintel A, Chandna A, Heyderman RS. Community-acquired acute bacterial meningitis in adults: a clinical update. Br Med Bull 2019; 131:57-70. [PMID: 31556944 DOI: 10.1093/bmb/ldz023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Acute bacterial meningitis (ABM) in adults is associated with a mortality that may exceed 30%. Immunization programs have reduced the global burden; in the UK, declining incidence but persistently high mortality and morbidity mean that clinicians must remain vigilant. SOURCES OF DATA A systematic electronic literature search of PubMed was performed to identify all ABM literature published within the past 5 years. AREAS OF AGREEMENT AND CONTROVERSY Clinical features cannot reliably distinguish between ABM and other important infectious and non-infectious aetiologies. Prompt investigation and empirical treatment are imperative. Lumbar puncture (LP) and cerebrospinal fluid microscopy, biochemistry and culture remain the mainstay of diagnosis, but molecular techniques are increasingly useful. The 2016 UK joint specialist societies' guideline provides expert recommendations for the management of ABM, yet published data suggest clinical care delivered in the UK is frequently not adherent. Anxiety regarding risk of cerebral herniation following LP, unnecessary neuroimaging, underutilization of molecular diagnostics and suboptimal uptake of adjunctive corticosteroids compromise management. GROWING POINTS There is increasing recognition that current antibiotic regimens and adjunctive therapies alone are insufficient to reduce the mortality and morbidity associated with ABM. AREAS TIMELY FOR DEVELOPING RESEARCH Research should be focused on optimization of vaccines (e.g. pneumococcal conjugate vaccines with extended serotype coverage), targeting groups at risk for disease and reservoirs for transmission; improving adherence to management guidelines; development of new faster, more accurate diagnostic platforms (e.g. novel point-of-care molecular diagnostics); and development of new adjunctive therapies (aimed at the host-inflammatory response and bacterial virulence factors).
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Affiliation(s)
- Jayne Ellis
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, 235 Euston Rd, Bloomsbury, London, UK
| | - Akish Luintel
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, 235 Euston Rd, Bloomsbury, London, UK
| | - Arjun Chandna
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, 235 Euston Rd, Bloomsbury, London, UK
| | - Robert S Heyderman
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, 235 Euston Rd, Bloomsbury, London, UK
- Division of Infection and Immunity, University College London, Rayne Building, 5 University Street, London, UK
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Moosavian M, Seyed-Mohammadi S, Saki M, Shahi F, Khoshkholgh Sima M, Afshar D, Barati S. Loop-mediated isothermal amplification for detection of Legionella pneumophila in respiratory specimens of hospitalized patients in Ahvaz, southwest Iran. Infect Drug Resist 2019; 12:529-534. [PMID: 30881058 PMCID: PMC6402708 DOI: 10.2147/idr.s198099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Legionnaires’ disease is an important public health problem that can cause substantial mortality and morbidity. Legionnaires’ disease-risk estimation may be compromised by uncertainties in Legionella-detection methods. The aim of this study was the detection of L. pneumophila in respiratory specimens of hospitalized patients with respiratory symptoms by culture, PCR, and loop-mediated isothermal amplification (LAMP) methods. Methods Sputum and bronchoalveolar lavage samples were obtained from patients with pneumonia admitted to teaching hospitals in Ahvaz, Iran from June 2016 to March 2017. Isolation of Legionella spp. was done by culturing the samples directly onto buffered charcoal–yeast extract and modified Wadowsky–Yee agar medium. Then, PCR and LAMP assays were performed for detection of L. pneumophila via its mip gene in respiratory specimens. Results A total of 100 respiratory specimens were collected. Our results showed that 1% of the samples were culture positive for Legionella spp., and 3% and 7% of samples were positive for L. pneumophila using the mip gene on PCR and LAMP assays, respectively. Conclusion Legionnaires’ disease should be considered in the diagnosis of pulmonary infectious diseases. Also, the LAMP assay is a faster method with higher sensitivity and specificity than conventional methods, such as PCR and culture, for laboratory diagnosis of Legionnaires’ disease.
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Affiliation(s)
- Mojtaba Moosavian
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Sakineh Seyed-Mohammadi
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran, .,Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran, .,Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Fatemeh Shahi
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran, .,Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Mahtab Khoshkholgh Sima
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Davoud Afshar
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Sara Barati
- Department of Pathobiology, School of Veterinary, University of Shahid Chamran, Ahvaz, Iran
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37
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Sui X, Zhang X, Fei D, Zhang Z, Ma M. Simultaneous rapid detection of Hantaan virus and Seoul virus using RT-LAMP in rats. PeerJ 2019; 6:e6068. [PMID: 30643674 PMCID: PMC6329334 DOI: 10.7717/peerj.6068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 11/04/2018] [Indexed: 12/18/2022] Open
Abstract
Background Hemorrhagic fever with renal syndrome is in most cases caused by the Hantaan virus (HTNV) and Seoul virus (SEOV). To develop and apply reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect HTNV and SEOV simultaneously, which was faster, more cost effective, and easier to perform as the target gene amplified rapidly. In this article an assay based on LAMP is demonstrated, which only employs such apparatus as a water bath or a heat block. Methods A chromogenic method using the calcein/Mn2+ complex and real-time turbidity monitoring method were used to assess reaction progress of the reaction, and the specificity of the RT-LAMP-based assay was assessed by detecting cDNAs/cRNAs generated from Coxsackievirus A16, Influenza virus, lymphocytic choriomeningitis virus, mouse poxvirus, rotavirus, mouse hepatitis virus. In addition, 23 clinical specimens were used to determine the agreement between the RT-LAMP assay with reverse transcriptase polymerase chain reaction (RT-PCR) and immunofluorescence (IFT) method. Results The detection limit of RT-LAMP to HNTV and SEOV was as low as 10 copies/μL with optimized reaction conditions, which was much more sensitive than the RT-PCR method (100–1,000 copies/μL). At the same time, the detection results of 23 clinical specimens have also illustrated the agreement between this the RT-LAMP assay with RT-PCR and IFT. Discussion This RT-LAMP assay could be used to perform simultaneous and rapid detection of HTNV and SEOV to the clinical specimens.
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Affiliation(s)
- Xin Sui
- Institute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, China.,The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Xu Zhang
- Institute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, China.,Microbiological Laboratory, Center for Disease Control and Prevention of Jinzhou, Jinzhou, Liaoning, China
| | - Dongliang Fei
- Institute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Zhen Zhang
- Microbiological Laboratory, Center for Disease Control and Prevention of Jinzhou, Jinzhou, Liaoning, China
| | - Mingxiao Ma
- Institute of Biological Sciences, Jinzhou Medical University, Jinzhou, Liaoning, China
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38
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Bannister SA, Kidd SP, Kirby E, Shah S, Thomas A, Vipond R, Elmore MJ, Telfer Brunton A, Marsh P, Green S, Silman NJ, Kempsell KE. Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species. High Throughput 2018; 7:ht7040032. [PMID: 30332776 PMCID: PMC6306750 DOI: 10.3390/ht7040032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/11/2018] [Accepted: 09/21/2018] [Indexed: 02/03/2023] Open
Abstract
Meningitis is commonly caused by infection with a variety of bacterial or viral pathogens. Acute bacterial meningitis (ABM) can cause severe disease, which can progress rapidly to a critical life-threatening condition. Rapid diagnosis of ABM is critical, as this is most commonly associated with severe sequelae with associated high mortality and morbidity rates compared to viral meningitis, which is less severe and self-limiting. We have designed a microarray for detection and diagnosis of ABM. This has been validated using randomly amplified DNA targets (RADT), comparing buffers with or without formamide, in glass slide format or on the Alere ArrayTubeTM (Alere Technologies GmbH) microarray platform. Pathogen-specific signals were observed using purified bacterial nucleic acids and to a lesser extent using patient cerebral spinal fluid (CSF) samples, with some technical issues observed using RADT and glass slides. Repurposing the array onto the Alere ArrayTubeTM platform and using a targeted amplification system increased specific and reduced nonspecific hybridization signals using both pathogen nucleic and patient CSF DNA targets, better revealing pathogen-specific signals although sensitivity was still reduced in the latter. This diagnostic microarray is useful as a laboratory diagnostic tool for species and strain designation for ABM, rather than for primary diagnosis.
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Affiliation(s)
| | - Stephen P Kidd
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | | | - Sonal Shah
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Anvy Thomas
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Richard Vipond
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | | | - Andrew Telfer Brunton
- Department of Clinical Microbiology, Royal Cornwall Hospitals NHS Trust, Penventinnie Lane, Treliske, Truro, Cornwall TR1 3LQ, UK.
| | - Peter Marsh
- Public Health England Laboratory Southampton, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.
| | - Steve Green
- Public Health England Laboratory Southampton, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.
| | - Nigel J Silman
- Public Health England, Porton Down, Salisbury SP4 0JG, UK.
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