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Wen XH, Han YL, Cao XS, Zhao W, Yan Z, Yan L, Wen JX, Hu ZD, Zheng WQ. Diagnostic value of nucleic acid amplification tests for tuberculous pleural effusion. Future Microbiol 2023; 18:971-983. [PMID: 37702019 DOI: 10.2217/fmb-2023-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
Diagnosing tuberculous pleural effusion (TPE) is challenging for pulmonologists and laboratory scientists. The gold standards for TPE diagnosis are pleural fluid Ziehl-Neelsen staining, Mycobacterium tuberculosis (Mtb) culture and pleural biopsy. These tools have limitations, including low sensitivity, long turnaround time and invasiveness. The nucleic acid amplification test (NAAT) is a rapid and minimally invasive tool for diagnosing TPE. This review summarizes the diagnostic accuracy of available NAATs for TPE, with a focus on the evidence from systematic reviews and meta-analyses. The NAATs summarized in this review include in-house NAATs, GeneXpert-MTB/RIF, GeneXpert-MTB/RIF Ultra, simultaneous amplification and testing-tuberculosis, FluoroType MTB and loop-mediated isothermal amplification.
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Affiliation(s)
- Xu-Hui Wen
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
- Department of Parasitology, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Yu-Ling Han
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
- Department of Parasitology, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Xi-Shan Cao
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Wen Zhao
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Zhi Yan
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
- Department of Parasitology, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Li Yan
- Department of Respiratory & Critical Care Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Jian-Xun Wen
- Department of Medical Experiment Center, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Zhi-De Hu
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Wen-Qi Zheng
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
- Department of Parasitology, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
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de Sousa KAF, Nonaka CKV, Khouri R, Gurgel Rocha CA, Regis-Silva CG, de Freitas Souza BS. Rapid Detection of SARS-CoV-2 Based on the LAMP Assay Associated with the CRISPRCas12a System. Diagnostics (Basel) 2023; 13:2233. [PMID: 37443626 DOI: 10.3390/diagnostics13132233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The global public health system has been severely tested by the COVID-19 pandemic. Mass testing was essential in controlling the transmission of the SARS-CoV-2; however, its implementation has encountered challenges, particularly in low-income countries. The urgent need for rapid and accurate tests for SARS-CoV-2 has proven to be extremely important. Point-of-care tests using the CRISPR system for COVID-19 have shown promise, with a reported high sensitivity and rapid detection. The performance of a CRISPR-based SARS-CoV-2 testing system was reported in this study. METHODS A total of 29 nasopharyngeal samples were evaluated, including 23 samples from individuals suspected of COVID-19, and six samples positive for H3N2 or respiratory syncytial virus. Two reference samples with known concentrations of SARS-CoV-2 RNA (3000 RNA copies/mL) or viral titer determined by plaque assay (105 PFU/mL) were also evaluated. The LAMP technique was employed to amplify the ORF1ab gene and the results were analyzed using a Gemini XPS fluorescence reader. RESULTS The RT-LAMP-CRISPR/Cas12 assay showed 100% concordance compared to RT-PCR. The RT-PCR presented a detection limit of 0.01 PFU/mL and the CRISPR/Cas12 system showed a limit of 15.6 PFU/mL. The RT-PCR sensitivity was approximately 8 RNA copies/µL and CRISPR/Cas12 at 84 RNA copies/µL. CONCLUSION The RT-LAMP-CRISPR/Cas12a assay offered a promising alternative for the detection of SARS-CoV-2 and reinforces that CRISPR-based diagnostic techniques can be an alternative for fast and accurate assays.
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Affiliation(s)
- Karoline Almeida Felix de Sousa
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador 40296-710, Brazil
- Center for Biotechnology and Cell Therapy, D'Or Institute for Research and Education (IDOR), Salvador 41253-190, Brazil
| | - Carolina Kymie Vasques Nonaka
- Center for Biotechnology and Cell Therapy, D'Or Institute for Research and Education (IDOR), Salvador 41253-190, Brazil
- São Rafael Hospital, Salvador 41253-190, Brazil
| | - Ricardo Khouri
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador 40296-710, Brazil
- Faculty of Medicine, Federal University of Bahia, Salvador 40210-630, Brazil
| | - Clarissa Araújo Gurgel Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador 40296-710, Brazil
- Center for Biotechnology and Cell Therapy, D'Or Institute for Research and Education (IDOR), Salvador 41253-190, Brazil
- Faculty of Medicine, Federal University of Bahia, Salvador 40210-630, Brazil
- Faculty of Dentistry, Federal University of Bahia, Salvador 40210-630, Brazil
| | | | - Bruno Solano de Freitas Souza
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador 40296-710, Brazil
- Center for Biotechnology and Cell Therapy, D'Or Institute for Research and Education (IDOR), Salvador 41253-190, Brazil
- São Rafael Hospital, Salvador 41253-190, Brazil
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Kim HN, Lee J, Yoon SY, Jang WS, Lim CS. Rapid Detection of Mycobacterium Tuberculosis Using a Novel Point-of-Care BZ TB/NTM NALF Assay: Integrating LAMP and LFIA Technologies. Diagnostics (Basel) 2023; 13:diagnostics13081497. [PMID: 37189598 DOI: 10.3390/diagnostics13081497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Tuberculosis (TB) is one of the leading causes of infectious mortality from a single infectious agent, Mycobacterium tuberculosis (MTB). This study evaluated the performance of the newly developed BZ TB/NTM NALF assay, which integrated loop-mediated isothermal amplification and lateral flow immunochromatographic assay technologies, for the detection of MTB. A total of 80 MTB-positive samples and 115 MTB-negative samples were collected, all of which were confirmed by TB real-time PCR (RT-PCR) using either AdvanSureTM TB/NTM RT-PCR Kit or Xpert® MTB/RIF Assay. The performance of the BZ TB/NTM NALF assay was evaluated by calculating its sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) in comparison to those of the RT-PCR methods. Compared to the RT-PCR, the sensitivity, specificity, PPV, and NPV of BZ TB/NTM NALF assay were 98.7%, 99.1%, 98.7%, and 99.1%, respectively. The concordance rate between BZ TB/NTM NALF and RT-PCR was 99.0%. Rapid and simple detection of MTB is essential for global case detection and further elimination of TB. The performance of the BZ TB/NTM NALF Assay is acceptable with a high concordance with RT-PCR, indicating that it is reliable for use in a low-resource environment.
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Affiliation(s)
- Ha Nui Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Junmin Lee
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Soo-Young Yoon
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Woong Sik Jang
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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Kadivarian S, Rostamian M, Kooti S, Abiri R, Alvandi A. Diagnostic accuracy of gold nanoparticle combined with molecular method for detection of Mycobacterium tuberculosis: A systematic review and meta-analysis study. SENSING AND BIO-SENSING RESEARCH 2023. [DOI: 10.1016/j.sbsr.2023.100559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
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Huertas-López A, Álvarez-García G, Sánchez-Sánchez R, Cantos-Barreda A, Ibáñez-López FJ, Martínez-Subiela S, Cerón JJ, Martínez-Carrasco C. A systematic review and meta-analysis of the serological diagnosis of Toxoplasma gondii infection highlight the lack of a One Health integrative research. Res Vet Sci 2023; 155:137-149. [PMID: 36682338 DOI: 10.1016/j.rvsc.2023.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/27/2022] [Accepted: 01/05/2023] [Indexed: 01/12/2023]
Abstract
Toxoplasma gondii is a globally distributed food-borne zoonotic parasite with numerous infection sources. The control of this zoonosis requires a One Health response that partially depends on serological monitoring in humans and animals. Herein, a systematic review and a meta-analysis were performed to analyse and compare the transdisciplinary and integrative research under the One Health approach. We searched for articles published between January 1st 2014 and September 5th 2022, focused on the development and evaluation of serological techniques for the diagnosis of T. gondii infection in humans and animals. After an exhaustive search on three scientific databases, a quality assessment was performed on 291 articles by QUADAS-2 tool, and 113 articles were finally selected. A total of 18 variables were extracted and analysed, including bibliometric characteristics, study aims and methodology. Remarkably, none of the studies included in the meta-analysis explicitly quoted the words "One Health", and only 23.9% of them alluded to the principles underlying the One Health approach; in particular, none were conducted by physician-only teams, with the majority of these studies involving interdisciplinary research teams, followed by veterinarians and by non-physician or non-veterinarian researchers. The One Health approach followed in the serodiagnosis of T. gondii still needs further integration among scientific disciplines, which is essential to design effective control strategies.
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Affiliation(s)
- Ana Huertas-López
- Interdisciplinary Laboratory of Clinical Analysis, Interlab-UMU, University of Murcia - Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Espinardo, Murcia, Spain
| | - Gema Álvarez-García
- Animal Health Department, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain.
| | - Roberto Sánchez-Sánchez
- Animal Health Department, Complutense University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Ana Cantos-Barreda
- Department of Biochemistry and Molecular Biology-A, University of Murcia - Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Espinardo, Murcia, Spain; Animal Health Department, University of Murcia - Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Espinardo, Murcia, Spain
| | - Francisco Javier Ibáñez-López
- Statistical Support Section (SAE), Scientific and Research Area (ACTI), University of Murcia - Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Espinardo, Murcia, Spain
| | - Silvia Martínez-Subiela
- Interdisciplinary Laboratory of Clinical Analysis, Interlab-UMU, University of Murcia - Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Espinardo, Murcia, Spain
| | - José Joaquín Cerón
- Interdisciplinary Laboratory of Clinical Analysis, Interlab-UMU, University of Murcia - Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Espinardo, Murcia, Spain
| | - Carlos Martínez-Carrasco
- Animal Health Department, University of Murcia - Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Espinardo, Murcia, Spain
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Bumbrah GS, Jain S, Fatima Z, Hameed S. Efficacy of LAMP assay for Mycobacterial spp. detection to prevent treatment delays and onset of drug resistance: a systematic review and meta-analysis. Drug Target Insights 2023; 17:78-89. [PMID: 37304408 PMCID: PMC10249090 DOI: 10.33393/dti.2023.2596] [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: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Background Tuberculosis (TB) remains a deadly disease affecting one-third population globally. Long turnaround time and poor sensitivity of the conventional diagnostics are the major impediments for faster diagnosis of Mycobacterial spp to prevent drug resistance. To overcome these issues, molecular diagnostics have been developed. They offer enhanced sensitivity but require sophisticated infrastructure, skilled manpower and remain expensive. Methods In that context, loop-mediated isothermal amplification (LAMP) assay, recommended by the WHO in 2016 for TB diagnosis, sounds as a promising alternative that facilitates visual read outs. Therefore, the aim of the present study is to conduct a meta-analysis to assess the diagnostic efficiency of LAMP for the detection of a panel of Mycobacterium spp. following PRISMA guidelines using scientific databases. From 1600 studies reported on the diagnosis of Mycobacterium spp., a selection of 30 articles were identified as eligible to meet the criteria of LAMP based diagnosis. Results It was found that most of the studies were conducted in high disease burden nations such as India, Thailand, and Japan with sputum as the most common specimen to be used for LAMP assay. Furthermore, IS6110 gene and fluorescence-based detections ranked as the most used target and method respectively. The accuracy and precision rates mostly varied between 79.2% to 99.3% and 73.9% to 100%, respectively. Lastly, a quality assessment based on QUADAS-2 of bias and applicability was conducted. Conclusion LAMP technology could be considered as a feasible alternative to current diagnostics considering high burden for rapid testing in low resource regions.
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Affiliation(s)
- Gurvinder Singh Bumbrah
- Department of Forensic Sciences, Amity School of Applied Sciences, Amity University Haryana, Gurugram, Manesar - India
| | - Sarika Jain
- Department of Mathematics, Amity School of Applied Sciences, Amity University Haryana, Gurugram, Manesar - India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar - India
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha - Saudi Arabia
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar - India
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Lin JJ, Xi XH, Xia L, Tan YJ, Chen Y, Di HQ, Chen ZH, Yu T, Wei JH, Fang P, Lin XM, Su BY, Yan MZ, Yu YM, Okada K, Noguchi N, Annaka T, Liu XH, Lu SH. Diagnostic accuracy of loop-mediated isothermal amplification for pulmonary tuberculosis in China. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.1046948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ObjectivesTo evaluate the diagnostic accuracy of Loop-Mediated Isothermal Amplification Platform (LAMP) in detecting pulmonary tuberculosis (PTB).MethodsThis multicenter prospective study was conducted at six sites in China from June, 2018 to December, 2019. Patients with suspected PTB were consecutively recruited and respiratory samples were collected from all patients. LAMP, Xpert MTB/RIF assay (Xpert), fluorescence smear microscopy, and BACTEC MGIT 960 liquid culture (Mtb culture) were performed for each sample. Diagnostic accuracy indices were calculated against Mtb culture results.ResultsA total of 845 participants were enrolled, but only 799 were included in the analysis. The sensitivities of LAMP, Xpert, and smear microscopy were 78.6% (239/304), 82.2% (250/304), and 63.8% (194/304), respectively, and their specificities were 88.7% (439/495), 86.1% (426/495), and 94.9% (470/495), respectively. The LAMP assay showed substantial agreement with other tests (kappa 0.64–0.79).ConclusionThe LAMP assay performs as well as Xpert MTB/RIF assay and Mtb culture in tertiary-care hospitals. It can be used as an alternative test for detecting PTB with the advantages of being fast, inexpensive, and easy to operate.
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Atçeken N, Yigci D, Ozdalgic B, Tasoglu S. CRISPR-Cas-Integrated LAMP. BIOSENSORS 2022; 12:1035. [PMID: 36421156 PMCID: PMC9688180 DOI: 10.3390/bios12111035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Pathogen-specific point-of-care (PoC) diagnostic tests have become an important need in the fight against infectious diseases and epidemics in recent years. PoC diagnostic tests are designed with the following parameters in mind: rapidity, accuracy, sensitivity, specificity, and ease of use. Molecular techniques are the gold standard for pathogen detection due to their accuracy and specificity. There are various limitations in adapting molecular diagnostic methods to PoC diagnostic tests. Efforts to overcome limitations are focused on the development of integrated molecular diagnostics by utilizing the latest technologies available to create the most successful PoC diagnostic platforms. With this point of view, a new generation technology was developed by combining loop-mediated isothermal amplification (LAMP) technology with clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) technology. This integrated approach benefits from the properties of LAMP technology, namely its high efficiency, short turnaround time, and the lack of need for a complex device. It also makes use of the programmable function of CRISPR-Cas technology and the collateral cleavage activity of certain Cas proteins that allow for convenient reporter detection. Thus, this combined technology enables the development of PoC diagnostic tests with high sensitivity, specificity, and ease of use without the need for complicated devices. In this review, we discuss the advantages and limitations of the CRISPR/Cas combined LAMP technology. We review current limitations to convert CRISPR combined LAMP into pathogen-specific PoC platforms. Furthermore, we point out the need to design more useful PoC platforms using microfabrication technologies by developing strategies that overcome the limitations of this new technology, reduce its complexity, and reduce the risk of contamination.
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Affiliation(s)
- Nazente Atçeken
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Defne Yigci
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Berin Ozdalgic
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Department of Mechanical Engineering, Engineering Faculty, Koç University, Istanbul 34450, Turkey
- School of Medical Services & Techniques, Dogus University, Istanbul 34775, Turkey
| | - Savas Tasoglu
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Department of Mechanical Engineering, Engineering Faculty, Koç University, Istanbul 34450, Turkey
- Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Istanbul 34684, Turkey
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Istanbul 34450, Turkey
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Guo YL, Wang SS, Jiang GL, Ban WJ, Liu Y. Evaluation of the diagnostic value of loop-mediated isothermal amplification assays targeting three different Mycobacterium tuberculosis genes. J Microbiol Methods 2022; 200:106547. [PMID: 35926680 DOI: 10.1016/j.mimet.2022.106547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/16/2022] [Accepted: 07/29/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND The aim of the study was to evaluate a loop-mediated isothermal amplification (LAMP) assay for the ability to diagnose tuberculosis directly from clinical samples rapidly. METHODS LAMP assays were performed using previously reported primer sets to amplify three specific Mycobacterium tuberculosis (MTB) gene targets, hspX, gyrB, and IS6110. Quantitated DNA from strain H37Rv were detected for assessment of analytical sensitivity; specificity was evaluated by testing eight species of non-tuberculosis Mycobacterium (NTM) and four unrelated bacterial species. Sputum samples from 68 pulmonary tuberculosis patients and a control group consisting of 45 lung cancer patients and 20 healthy controls were analyzed using LAMP assays, and then compared with smear, culture and quantitative real-time PCR (qRT-PCR) methods. RESULTS All three LAMP assays showed 100% specificity for MTB when tested against NTM and other bacterial species. The gyrB-LAMP assay was able to detect 60 cfu/ml of H37Rv suspension within 1 h, similar to qRT-PCR, but 10 times more sensitive than the hspX-LAMP and IS6110-LAMP assays. In clinical samples, when qRT-PCR was used as the reference method, the sensitivity of the three LAMP assays targeting hspX, gyrB, and IS6110 genes was 94.6, 98.2 and 92.9%, respectively. CONCLUSIONS LAMP is more sensitive than smear microscopy and close to qRT-PCR in sensitivity for the detection of MTB. LAMP has comparable specificity to qRT-PCR but was more rapid and convenient.
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Affiliation(s)
- Yan-Ling Guo
- Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Sai-Sai Wang
- Disease Prevention and Control Department, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China
| | - Guang-Lu Jiang
- National Tuberculosis Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China
| | - Wu-Juan Ban
- Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Yang Liu
- Disease Prevention and Control Department, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149,China.
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Development and application of LAMP assays for the detection of enteric adenoviruses in feces. Microbiol Spectr 2022; 10:e0051622. [PMID: 35862966 PMCID: PMC9430467 DOI: 10.1128/spectrum.00516-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is an alternative to PCR that is faster and requires fewer resources. Here, we describe two LAMP assays for the detection of human adenoviruses in the feces of children with acute intestinal infections. We designed сolorimetric LAMP (c-LAMP) and real-time LAMP (f-LAMP) with fluorescent probes to detect the DNA of the adenovirus F human adenovirus 40/41 (hAdV40/41) hexon gene. The detection limit of both developed methods was 103 copies/mL, which is comparable to the sensitivity of PCR. The specificities of both c-LAMP and f-LAMP were high, with no false-positive results for clinical samples that do not contain adenovirus F, when testing other viruses and microorganisms. Comparative tests of PCR and LAMP on clinical samples from patients with acute gastroenteritis were carried out. For all samples with a PCR threshold cycle (CT) of up to 36, the PCR and LAMP results completely coincided; however, at low viral loads, the diagnostic sensitivity of LAMP, especially c-LAMP with colorimetric detection, was inferior to that of PCR. The combination of LAMP with modern methods of nucleic acid extraction, both in manual and automatic modes, can reduce the time for a complete study, including extraction of nucleic acid material and amplification, to 60 min. IMPORTANCE In April 2022, several cases of acute hepatitis of unknown origin were reported in children from 12 countries. In many cases, enteric adenovirus or SARS-CoV-2 and adenovirus coinfection were detected. It is known that human adenoviruses can cause different infections of varying severity, from asymptomatic to severe cases with lethal outcomes. There is a need to increase the diagnostic capabilities of clinical laboratories to identify such an underestimated pathogen as adenovirus. Although PCR remains the gold standard for pathogen detection, this method requires specialized equipment and has a long turnaround time to process samples. Previously, LAMP assays for the detection of human adenovirus have been based on measuring the turbidity, the fluorescence of intercalated dyes, or electrophoretic separation. Herein, we present LAMP-based assays with colorimetric or fluorescent detection and perform a detailed assessment of their sensitivity, specificity, and diagnostic performance.
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Kham-Kjing N, Ngo-Giang-Huong N, Tragoolpua K, Khamduang W, Hongjaisee S. Highly Specific and Rapid Detection of Hepatitis C Virus Using RT-LAMP-Coupled CRISPR-Cas12 Assay. Diagnostics (Basel) 2022; 12:diagnostics12071524. [PMID: 35885430 PMCID: PMC9317538 DOI: 10.3390/diagnostics12071524] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 12/23/2022] Open
Abstract
Hepatitis C virus (HCV) infection can be cured with pan-genotypic direct-acting antiviral agents. However, identifying individuals with current hepatitis C remains a major challenge, especially in resource-limited settings where access to or availability of molecular tests is still limited. The goal of this study was to develop and validate a molecular assay for the rapid detection of HCV RNA in resource-limited settings. It is based on a combination of reverse transcription loop-mediated isothermal amplification (RT-LAMP) with the clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 12a (CRISPR–Cas12a) cleavage assay that allows the recognition of specific HCV nucleic acid sequences. Amplified products after the cleavage reactions can be visualized on lateral flow strips or measured with a fluorescence detector. When tested on clinical samples from individuals infected with HCV, HIV, or HBV, or from healthy donors, the RT-LAMP-coupled CRISPR–Cas12 assay yielded 96% sensitivity, 100% specificity, and 97% agreement as compared to the reference method (Roche COBAS AmpliPrep/COBAS TaqMan HCV Test). This assay could detect HCV RNA concentrations as low as 10 ng/µL (an estimated 2.38 Log10 IU/mL). Therefore, this sensitive and specific assay may represent an affordable and reliable point-of-care test for the identification of individuals with active hepatitis C in low-resource settings.
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Affiliation(s)
- Nang Kham-Kjing
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (K.T.)
| | - Nicole Ngo-Giang-Huong
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle (MIVEGEC), Agropolis University Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Pour le Développement (IRD), 34394 Montpellier, France;
- Associated Medical Sciences (AMS)-PHPT Research Collaboration, Chiang Mai 50200, Thailand
| | - Khajornsak Tragoolpua
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (K.T.)
- Infectious Diseases Research Unit, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Woottichai Khamduang
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (K.T.)
- Associated Medical Sciences (AMS)-PHPT Research Collaboration, Chiang Mai 50200, Thailand
- Infectious Diseases Research Unit, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (W.K.); (S.H.)
| | - Sayamon Hongjaisee
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (W.K.); (S.H.)
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Saito Y, Matsui A, Michiyuki S, Morooka H, Ibi T, Yamauchi Y, Takahashi N, Shimizu Y, Ikeya T, Hoshi E, Sakao Y, Kawamura M. Loop-Mediated Isothermal Amplification as Point-of-Care Testing for EGFR-Mutated Lung Adenocarcinoma. MICROMACHINES 2022; 13:mi13060897. [PMID: 35744511 PMCID: PMC9230792 DOI: 10.3390/mi13060897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022]
Abstract
Liquid biopsy has been adapted as a diagnostic test for EGFR mutations in patients with advanced or metastatic non-small cell lung cancer (NSCLC). Loop-mediated isothermal amplification (LAMP) has been widely used for the rapid detection of pathogens through DNA amplification. This study investigated the efficacy of an EGFR-LAMP assay using plasma samples of patients with resected NSCLC tumors. The EGFR status was investigated using both LAMP and next-generation sequencing (NGS) assays in cases that met the following criteria: (1) pulmonary adenocarcinoma with EGFR mutation detected by the Therascreen EGFR PCR Kit and (2) preoperative plasma samples contained enough DNA for the LAMP and NGS experiments. Among 51 specimens from patients with EGFR-mutated tumors or metastatic lymph nodes, the LAMP assay detected 1 EGFR mutation that was also detected in the NGS assay. However, a plasma sample that demonstrated EGFR wild type in the LAMP assay showed an EGFR mutant status in NGS. The detection rates (1.9% in LAMP and 3.9% in NGS) were very low in both assays, demonstrating a similar performance in detecting EGFR mutations in NSCLC tumors; therefore, it could be a more suitable test for the advanced stage, not the early stage. Notably, the LAMP assay was more time-saving, cost-effective, and straightforward. However, further investigation is required to develop a more sensitive assay.
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Affiliation(s)
- Yuichi Saito
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku 173-8605, Tokyo, Japan; (Y.Y.); (Y.S.); (M.K.)
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
- Correspondence: ; Tel.: +81-33-964-1211; Fax: +81-33-964-6888
| | - Atsuka Matsui
- Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., 1381-3 Shimoishigami, Otawara-shi 324-0036, Tochigi, Japan; (A.M.); (S.M.)
| | - Satoru Michiyuki
- Biochemical Research Laboratory II, Eiken Chemical Co., Ltd., 1381-3 Shimoishigami, Otawara-shi 324-0036, Tochigi, Japan; (A.M.); (S.M.)
| | - Hiroaki Morooka
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Takayuki Ibi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Yoshikane Yamauchi
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku 173-8605, Tokyo, Japan; (Y.Y.); (Y.S.); (M.K.)
| | - Nobumasa Takahashi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Yoshihiko Shimizu
- Department of Pathology, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan;
| | - Tomohiko Ikeya
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Eishin Hoshi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, 1696 Itai, Kumagaya 360-0197, Saitama, Japan; (H.M.); (T.I.); (N.T.); (T.I.); (E.H.)
| | - Yukinori Sakao
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku 173-8605, Tokyo, Japan; (Y.Y.); (Y.S.); (M.K.)
| | - Masafumi Kawamura
- Department of Surgery, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku 173-8605, Tokyo, Japan; (Y.Y.); (Y.S.); (M.K.)
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13
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Bhatt A, Fatima Z, Ruwali M, Misra CS, Rangu SS, Rath D, Rattan A, Hameed S. CLEVER assay: A visual and rapid RNA extraction free detection of SARS-CoV-2 based on CRISPR-Cas integrated RT-LAMP technology. J Appl Microbiol 2022; 133:410-421. [PMID: 35396760 PMCID: PMC9111511 DOI: 10.1111/jam.15571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/28/2022]
Abstract
Aim The current scenario of COVID‐19 pandemic has presented an almost insurmountable challenge even for the most sophisticated hospitals equipped with modern biomedical technology. There is an urgency to develop simple, fast and highly accurate methods for the rapid identification and isolation of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infected patients. To address the ongoing challenge, the present study offers a CLEVER assay (CRISPR‐Cas integrated RT‐LAMP Easy, Visual and Extraction‐free RNA) which will allow RNA extraction‐free method to visually diagnose COVID‐19. RNA extraction is a major hurdle in preventing rapid and large‐scale screening of samples particularly in low‐resource regions because of the logistics and costs involved. Method and Result Herein, the visual SARS‐CoV‐2 detection method consists of RNA extraction‐free method directly utilizing the patient's nasopharyngeal and oropharyngeal samples for reverse transcription loop‐mediated isothermal amplification (RT‐LAMP). Additionally, the assay also utilizes the integration of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)‐Cas12‐based system using different guide RNAs of N, E and an internal control POP7 (human RNase P) genes along with visual detection via lateral flow readout‐based dip sticks with unaided eye (~100 min). Overall, the clinical sensitivity and specificity of the CLEVER assay were 89.6% and 100%, respectively. Conclusion Together, our CLEVER assay offers a point‐of‐care tool with no equipment dependency and minimum technical expertise requirement for COVID‐19 diagnosis. Significance and Impact of the Study To address the challenges associated with COVID‐19 diagnosis, we need a faster, direct and more versatile detection method for an efficient epidemiological management of the COVID‐19 outbreak. The present study involves developing a method for detection of SARS‐CoV‐2 in human body without RNA isolation step that can visually be detected with unaided eye. Taken together, our assay offers to overcome one major defect of the prior art, that is, RNA extraction step, which could limit the deployment of the previous assays in a testing site having limited lab infrastructure.
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Affiliation(s)
- Akansha Bhatt
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar), Haryana, India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar), Haryana, India
| | - Munindra Ruwali
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar), Haryana, India
| | - Chitra Seetharam Misra
- CRISPR Biology Group, Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Shyam Sunder Rangu
- CRISPR Biology Group, Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Devashish Rath
- CRISPR Biology Group, Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | | | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar), Haryana, India
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14
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Wu X, Chen Q, Yang C, Ning Q, Liu Z. An enhanced visual detection assay for Listeria monocytogenes in food based on isothermal amplified peroxidase-mimicking catalytic beacon. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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15
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Matthew MA, Christie J, Yang N, Yao C. A Loop-Mediated Isothermal Amplification (LAMP) Assay Specific to Trichomonas tenax Is Suitable for Use at Point-of-Care. Microorganisms 2022; 10:594. [PMID: 35336172 PMCID: PMC8949391 DOI: 10.3390/microorganisms10030594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
Trichomonas tenax is a flagellated protozoan that inhabits the human and canine oral cavity in patients with poor oral hygiene and periodontal disease. The loop-mediated isothermal amplification (LAMP) assay could provide clinicians with a quick, cheap and reliable diagnostic test used for the detection of T. tenax in various settings. In this study, we aimed to develop a LAMP assay that can detect T. tenax with high sensitivity and specificity. A set of LAMP primers were specifically designed to detect the ITS and 5.8S rRNA gene of T. tenax. The newly developed LAMP assay was 1000 times more sensitive than conventional PCR. The limit of detection of the LAMP assay was 10 fg of genomic DNA, or 0.2-1 cell. Moreover, the LAMP assay was specific, resulting in no cross-reaction even with a closely related protozoan T. vaginalis or other microorganisms (Streptococcus pyogenes, Staphylococcus aureus, Escherichia coli, Enterococcus faecalis, and Candida albicans) used. The present LAMP assay can be performed directly without prior DNA extraction, making the assay an easy, fast, cheap, specific and sensitive diagnostic tool for the detection of T. tenax at the point-of-care of both medical and veterinary clinics in developed and developing countries.
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Affiliation(s)
- Maurice A. Matthew
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre 00334, Saint Kitts and Nevis; (M.A.M.); (N.Y.)
- One Health Centre for Zoonosis and Tropical Veterinary Diseases, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre 00334, Saint Kitts and Nevis;
| | - Jevan Christie
- One Health Centre for Zoonosis and Tropical Veterinary Diseases, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre 00334, Saint Kitts and Nevis;
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre 00334, Saint Kitts and Nevis
| | - Nawu Yang
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre 00334, Saint Kitts and Nevis; (M.A.M.); (N.Y.)
- One Health Centre for Zoonosis and Tropical Veterinary Diseases, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre 00334, Saint Kitts and Nevis;
| | - Chaoqun Yao
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre 00334, Saint Kitts and Nevis; (M.A.M.); (N.Y.)
- One Health Centre for Zoonosis and Tropical Veterinary Diseases, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre 00334, Saint Kitts and Nevis;
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16
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Innovations in Molecular Identification of Mycobacterium tuberculosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant public health concern on a global scale. Quick and precise identification of Mycobacterium tuberculosis (MTB) in symptomatic patients is pivotal for worldwide TB eradication initiatives. As an infectious disorder induced by MTB, it remains a critical threat to public health, particularly in poor countries, due to an inadequate diagnostic research laboratory. There is a need for a persistent incentive to reduce response time for effective diagnosis and control of TB infection, which is a benefit that molecular techniques provide over traditional methods. Although there is a tremendous overall prevalence of TB and a relatively poor probability of case identification worldwide. Common screening techniques have focused on tests that have many fundamental shortcomings. Due to the development of antibiotic-resistant Mycobacterium strains, TB is one of the leading contributors to fatalities. It is now possible to examine TB using molecular detection techniques, which are faster and more cost-effective than previous methods, such as standard culture procedures to test and verify antibiotic resistance in patients with TB. Whole genome sequencing (WGS), faster nucleic acid amplification tests, has made it easier to diagnose and treat TB more quickly. This article addresses the genetic approaches for detecting Mycobacterium tuberculosis complex (MTBC) in clinical specimens as well as antibiotic resistance in mycobacterium and discusses the practical limitations of using these methods.
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17
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Jekloh N, Keawliam P, Mukem D, Rudeeaneksin J, Srisungngam S, Bunchoo S, Klayut W, Bhakdeenaun P, Phetsuksiri B. Evaluation of an in-house loop-mediated isothermal amplification for Mycobacterium tuberculosis detection in a remote reference laboratory, Thailand. Rev Inst Med Trop Sao Paulo 2022; 64:e57. [PMID: 36197418 PMCID: PMC9528361 DOI: 10.1590/s1678-9946202264057] [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: 03/03/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a simple and efficient nucleic acid amplification method for the rapid diagnosis of infectious diseases. This study assessed the performance of an in-house LAMP for tuberculosis (TB) diagnosis at a remote reference laboratory in the endemic setting of Thailand. As part of the routine service, 1,882 sputum samples were processed for mycobacterial culture in Lowenstein-Jensen and MGIT media. The DNA was extracted from the remaining decontaminated samples after the culture procedure for real-time polymerase chain reaction (PCR) analysis using Anyplex plus MTB/NTM detection kit. 785 (40.28%) were positive by mycobacterial culture. Of these, 222 DNA remnants were available and subjected to LAMP analysis. Based on culture as reference (Mycobacterium tuberculosis; MTB= 209/ non-tuberculous mycobacteria; NTM= 13), the overall sensitivity of LAMP and Anyplex plus assays for MTB detection were 89.95% (188/209; 95% confidential interval [CI]: 85.05-93.67%) and 96.65% (202/209; 95% CI: 93.22-98.64%), and the accuracy values were 88.74% (197/222; 95% CI: 83.83-92.58) and 96.40% (214/222; 93.02-98.43%), respectively. The sensitivity and accuracy of the in-house LAMP and the Anyplex plus real-time PCR assay were high in comparison to culture results. The high sensitivity and accuracy suggested that this in-house LAMP was promising and might be useful for early TB diagnosis.
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18
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Dahiya B, Kamra E, Alam D, Chauhan M, Mehta PK. Insight into diagnosis of female genital tuberculosis. Expert Rev Mol Diagn 2021; 22:625-642. [PMID: 34882522 DOI: 10.1080/14737159.2022.2016395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Female genital tuberculosis (TB) is a common manifestation of extrapulmonary TB (EPTB) with varied clinical presentations, i.e. infertility, pelvic pain and menstrual irregularities. Diagnosis of female genital TB is challenging predominantly due to paucibacillary nature of specimens and inconclusive results obtained by most of the routine laboratory tests. AREAS COVERED This review has briefly summarized the epidemiology, clinical features and transmission of female genital TB. Commonly used laboratory tests include bacteriological examination (smear/culture), tuberculin skin testing, interferon-γ release assays, imaging, laparoscopy/hysteroscopy and histopathological/cytological observations. Further, utility of nucleic acid amplification tests (NAATs), like loop-mediated isothermal amplification, PCR, multiplex-PCR, nested PCR, real-time PCR and GeneXpert® could significantly improve the detection of female genital TB. EXPERT OPINION Currently, there is no single test available for the efficient diagnosis of female genital TB, rather a combination of tests is being employed, which yields moderate diagnostic accuracy. The latest modalities developed for diagnosing pulmonary TB and other clinical EPTB forms, i.e. aptamer-linked immobilized sorbent assay, immuno-PCR (I-PCR), analysis of circulating cell-free DNA by NAATs, and identification of Mycobacterium tuberculosis biomarkers within extracellular vesicles of bodily fluids by I-PCR/nanoparticle-based I-PCR, may also be exploited to further improve the diagnosis of female genital TB.
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Affiliation(s)
- Bhawna Dahiya
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Ekta Kamra
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Danish Alam
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Meenakshi Chauhan
- Dept. of Obstetrics and Gynecology, Pt. B.D. Sharma University of Health Sciences, Rohtak-124001, Haryana, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
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19
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Hagos DG, Schallig HDFH, Kiros YK, Abdulkadir M, Wolday D. Performance of rapid rk39 tests for the diagnosis of visceral leishmaniasis in Ethiopia: a systematic review and meta-analysis. BMC Infect Dis 2021; 21:1166. [PMID: 34789175 PMCID: PMC8600897 DOI: 10.1186/s12879-021-06826-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022] Open
Abstract
Background Visceral Leishmaniasis (VL) is a severely neglected disease affecting millions of people with high mortality if left untreated. In Ethiopia, the primary laboratory diagnosis of VL is by using an antigen from a 39-amino acid sequence repeat of a kinesin-related (rK39) of leishmania donovani complex (L. donovani), rapid diagnostic tests (RDT). Different rk39 RDT brands are available with very variable performance and studies from Ethiopia showed a very wide range of sensitivity and specificity. Therefore, a systematic review and meta-analysis were conducted to determine the pooled sensitivity and specificity of rk39 RDT in Ethiopia. Method PUBMED, EMBASE, and other sources were searched using predefined search terms to retrieve all relevant articles from 2007 to 2020. Heterogeneity was assessed by visually inspecting summary receiver operating curves (SROC), Spearman correlation coefficient (rs), Cochran Q test statistics, inconsistency square (I2) and subgroup analysis. The presence and statistical significance of publication bias were assessed by Egger's test at p < 0.05, and all the measurements showed the presence of considerable heterogeneity. Quality assessment of diagnostic accuracy studies (QUADAS-2) checklists was used to check the qualities of the study. Results A total of 664 articles were retrieved, and of this 12 articles were included in the meta-analysis. Overall pooled sensitivity and specificity of the rk39 RDT to diagnose VL in Ethiopia were 88.0% (95% CI 86.0% to 89.0%) and 84.0% (95% CI 82.0% to 86.0%), respectively. The sensitivity and specificity of the rk39 RDT commercial test kits were DiaMed: 86.9% (95% CI 84.3% to 89.1%) and 82.2% (95% CI 79.3% to 85.0%), and InBios: 80.0% (95% CI 77.0% to 82.8%) and 97.4% (95% CI 95.0% to 98.8%), respectively. Conclusion Referring to our result, rk39 RDT considered an essential rapid diagnostic test for VL diagnosis. Besides to the diagnostic accuracy, the features such as easy to perform, quick (10–20 min), cheap, equipment-free, electric and cold chain free, and result reproducibility, rk39 RDT is advisable to remains in practice as a diagnostic test at least in the remote VL endemic localities till a better test will come.
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Affiliation(s)
- Dawit Gebreegziabiher Hagos
- College of Health Sciences, School of Medicine, Department of Medical Microbiology and Immunology, Mekelle University, Mekelle, Ethiopia. .,Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology, Experimental Parasitology Unit, Amsterdam University Medical Centres, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Henk D F H Schallig
- Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology, Experimental Parasitology Unit, Amsterdam University Medical Centres, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Yazezew K Kiros
- College of Health Sciences, School of Medicine, Department of Internal Medicine, Mekelle University, Mekelle, Ethiopia
| | - Mahmud Abdulkadir
- College of Health Sciences, School of Medicine, Department of Medical Microbiology and Immunology, Mekelle University, Mekelle, Ethiopia
| | - Dawit Wolday
- College of Health Sciences, School of Medicine, Mekelle University, Mekelle, Ethiopia
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20
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Mahas A, Wang Q, Marsic T, Mahfouz MM. A Novel Miniature CRISPR-Cas13 System for SARS-CoV-2 Diagnostics. ACS Synth Biol 2021; 10:2541-2551. [PMID: 34546709 PMCID: PMC8482783 DOI: 10.1021/acssynbio.1c00181] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Indexed: 12/12/2022]
Abstract
Rapid, point-of-care (POC) diagnostics are essential to mitigate the impacts of current (and future) epidemics; however, current methods for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) require complicated laboratory tests that are generally conducted off-site and require substantial time. CRISPR-Cas systems have been harnessed to develop sensitive and specific platforms for nucleic acid detection. These detection platforms take advantage of CRISPR enzymes' RNA-guided specificity for RNA and DNA targets and collateral trans activities on single-stranded RNA and DNA reporters. Microbial genomes possess an extensive range of CRISPR enzymes with different specificities and levels of collateral activity; identifying new enzymes may improve CRISPR-based diagnostics. Here, we identified a new Cas13 variant, which we named as miniature Cas13 (mCas13), and characterized its catalytic activity. We then employed this system to design, build, and test a SARS-CoV-2 detection module coupling reverse transcription loop-mediated isothermal amplification (RT-LAMP) with the mCas13 system to detect SARS-CoV-2 in synthetic and clinical samples. Our system exhibits sensitivity and specificity comparable to other CRISPR systems. This work expands the repertoire and application of Cas13 enzymes in diagnostics and for potential in vivo applications, including RNA knockdown and editing. Importantly, our system can be potentially adapted and used in large-scale testing for diverse pathogens, including RNA and DNA viruses, and bacteria.
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Affiliation(s)
- Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of
Biological Sciences, 4700 King Abdullah University of Science and
Technology, Thuwal 23955-6900, Saudi Arabia
| | - Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of
Biological Sciences, 4700 King Abdullah University of Science and
Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of
Biological Sciences, 4700 King Abdullah University of Science and
Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of
Biological Sciences, 4700 King Abdullah University of Science and
Technology, Thuwal 23955-6900, Saudi Arabia
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21
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Bhatt A, Fatima Z, Ruwali M, Hameed S. An inventory of diagnostic tools for detection of COVID-19. Curr Mol Med 2021; 22:608-620. [PMID: 34515000 DOI: 10.2174/1566524021666210910113714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/15/2021] [Accepted: 07/29/2021] [Indexed: 11/22/2022]
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-COV-2 has afflicted millions of lives globally and disrupted almost all the activities of mankind. Under such pressing circumstances when there are no effective therapeutics available, fast and accurate diagnosis of the corona virus is the only way out to limit the transmission. Since the inception of COVID-19, the demand of diagnostic tests has increased day by day and RT-PCR is the commonly used screening test which is not only time consuming but requires sophisticated resources. To address the increasing rate of spread of COVID-19, there is an urgent need of more diagnostic tools as the researches on vaccines is still at rudimentary level. This review summarizes an inventory on the diverse and currently available diagnostic methods based on nucleic acid and serology along with some of those working on novel principles viz. CRISPR, biosensors and NGS. Additionally, a gist of accessible diagnostic kits that are already approved by US & European authorities for the diagnosis of COVID-19 are also suggested that will help in selecting most effective tests under the given scenario. Taken together, this review will pave way for further strengthening the researches in the rapid and safer diagnostics of SARS-COV-2.
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Affiliation(s)
- Akansha Bhatt
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413. India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413. India
| | - Munindra Ruwali
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413. India
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar)-122413. India
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22
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Bayesian Statistics to Estimate Diagnostic Probability of Scaphoid Fractures from Clinical Examinations: A Meta-Analysis. Plast Reconstr Surg 2021; 147:424e-435e. [PMID: 33620933 DOI: 10.1097/prs.0000000000007627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Management of suspected scaphoid fractures includes repeated evaluation and casting in symptomatic patients with nondiagnostic radiographs. In this systematic review and meta-analysis, the authors compare the diagnostic accuracy of clinical examinations for scaphoid fractures and create a decision guide using Bayesian statistics. METHODS The MEDLINE, Embase, and Cumulative Index to Nursing and Allied Health Literature databases were queried for studies that evaluated clinical index tests and their diagnostic accuracies for scaphoid fracture. Summary estimates were achieved by a bivariate random effects model and used in Bayes' theorem. The authors varied the scaphoid fracture prevalence for sensitivity analysis. RESULTS Fourteen articles with 22 index tests and 1940 patients were included. Anatomical snuffbox pain/tenderness (11 studies, 1363 patients), pain with axial loading (eight studies, 995 patients), and scaphoid tubercle tenderness (five studies, 953 patients) had sufficient data for pooled analysis. Anatomical snuffbox pain/tenderness was the most sensitive test (0.93; 95 percent CI, 0.87 to 0.97), and pain with axial loading was the most specific test (0.66; 95 percent CI, 0.41 to 0.85), but all three tests had lower estimated specificities compared with sensitivities. In the base case, the probability of fracture was approximately 60 percent when a patient presented with all three findings after acute wrist injury. CONCLUSIONS The posttest probability of scaphoid fracture was sensitive to both prevalence and diagnostic accuracy of individual clinical index tests. In a population with a fracture prevalence of 20 percent, patients presenting with concurrent anatomical snuffbox pain/tenderness, pain on axial loading, and scaphoid tubercle tenderness may benefit from early advanced imaging to rule out scaphoid fractures if initial radiographs are nondiagnostic. CLINICAL QUESTION/LEVEL OF EVIDENCE Diagnostic, II.
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23
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Rahman MR, Hossain MA, Mozibullah M, Mujib FA, Afrose A, Shahed-Al-Mahmud M, Apu MAI. CRISPR is a useful biological tool for detecting nucleic acid of SARS-CoV-2 in human clinical samples. Biomed Pharmacother 2021; 140:111772. [PMID: 34062417 PMCID: PMC8156908 DOI: 10.1016/j.biopha.2021.111772] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/26/2022] Open
Abstract
The recent pandemic of novel coronavirus disease (COVID-19) has spread globally and infected millions of people. The quick and specific detection of the nucleic acid of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) remains a challenge within healthcare providers. Currently, quantitative reverse transcription-polymerase chain reaction (RT-qPCR) is the widely used method to detect the SARS-CoV-2 from the human clinical samples. RT-qPCR is expensive equipment and needs skilled personnel as well as lengthy detection time. RT-qPCR limitation needed an alternative healthcare technique to overcome with a fast and cheaper detection method. By applying the principles of CRISPR technology, several promising detection methods giving hope to the healthcare community. CRISPR-based detection methods include SHERLOCK-Covid, STOP-Covid, AIOD-CRISPR, and DETECTR platform. These methods have comparative advantages and drawbacks. Among these methods, AIOD-CRISPR and DETECTR are reasonably better diagnostic methods than the others if we compare the time taken for the test, the cost associated with each test, and their capability of detecting SARS-CoV-2 in the clinical samples. It may expect that the promising CRISPR-based methods would facilitate point-of-care (POC) applications in the CRISPR-built next-generation novel coronavirus diagnostics.
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Affiliation(s)
- Md Rashidur Rahman
- Department of Chemical Engineering, Kyushu University, Japan; Department of Pharmacy, Jashore University of Science and Technology, Bangladesh.
| | - Md Amjad Hossain
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Bangladesh
| | - Md Mozibullah
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Bangladesh
| | - Fateh Al Mujib
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Bangladesh
| | | | - Md Shahed-Al-Mahmud
- Department of Microbiology and Immunology, School of Medicine, Tzu Chi University, Hualien, Taiwan; Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Md Aminul Islam Apu
- Graduate School of International Agricultural Technology, Seoul National University, South Korea
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Morero M, Ramirez MR, Oyhenart J. Taguchi method for the optimization of three loop mediated isothermal amplification procedures for Tritrichomonas foetus detection. Vet Parasitol 2021; 295:109462. [PMID: 34058662 DOI: 10.1016/j.vetpar.2021.109462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022]
Abstract
Taguchi method was used to optimize loop mediated isothermal amplification tests aimed to amplify segments of the elongation factor 1a1 (tf-ef1a1), the 5,8 ribosomal gene (tf-5,8 r) or the beta tubulin 2 (tf-btub2) from the protozoan parasite Tritrichomonas foetus. L9 orthogonal array and quadratic loss functions that penalize deviations from prediction values revealed the effect of amplification reaction components. Analysis of variance (ANOVA) decomposed the contribution of individual factors to a small Ct. Confirmation experiments established that optimum conditions were predictable, verifiable and reproducible. Primers concentration conditioned the non-specific amplification of tf-ef1a1 while betaine and magnesium concentration contributed to accelerate the time to reach a positive threshold in tf-ef1a1, tf-5,8 r and tf-btub2. The general strategy of simple and robust experimental design holds potential as a general optimization protocol for LAMP tests in every diagnostic laboratory.
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Affiliation(s)
- Mariana Morero
- INCITAP, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Santa Rosa, La Pampa, Argentina
| | - María Rosana Ramirez
- CONICET, Instituto Universitario Fundación Hector Barceló, Santo Tomé, Corrientes, Argentina
| | - Jorge Oyhenart
- INCITAP, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Santa Rosa, La Pampa, Argentina.
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Loop-mediated isothermal amplification (LAMP) assay targeting RLEP for detection of Mycobacterium leprae in leprosy patients. Int J Infect Dis 2021; 107:145-152. [PMID: 33864913 DOI: 10.1016/j.ijid.2021.04.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Leprosy is a chronic infectious disease caused by Mycobacterium leprae and it remains a significant health problem in several parts of the world. Early and accurate diagnosis of this disease is therefore essential. Previously published loop-mediated isothermal amplification (LAMP) protocols for detecting mycobacterial species used conventional primers targeting the 16S rRNA, gyrB and insertion sequence genes. METHODS In this study, we conducted a LAMP assay for leprosy and compared it with quantitative polymerase chain reaction (q-PCR) and conventional PCR assays to determine the efficiency, sensitivity and specificity of each technique. We chose conserved sequence RLEP as a suitable molecular target for assays. RESULTS The LAMP assay provided rapid and accurate results, confirming leprosy in 91/110 clinical skin tissue samples from leprosy patients and amplifying the target pathogen in <60 min at 65 °C. The assay was more sensitive than conventional PCR and more straightforward and faster than the q-PCR assay. CONCLUSIONS The LAMP assay has the potential for developing quicker, more accessible visual methods for the detection of M. leprae, which will enable early diagnosis and treatment and prevent further infection in endemic areas.
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Saito Y, Takahashi N, Matsui A, Michiyuki S, Yamauchi Y, Shimizu Y, Hoshi E, Sakao Y, Kawamura M. Comparative study of the loop-mediated isothermal amplification method and the QIAGEN therascreen PCR kit for the detection of EGFR mutations in non-small cell lung cancer. J Thorac Dis 2021; 13:743-753. [PMID: 33717546 PMCID: PMC7947485 DOI: 10.21037/jtd-20-2642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Epidermal growth factor receptor (EGFR) mutations are important biomarkers in the treatment of patients with advanced or metastatic diseases. The therascreen EGFR Rotor-Gene Q (RGQ) PCR Kit® (Qiagen, Inc.) is an approved diagnostic test for EGFR mutations in non-small cell lung cancer (NSCLC). This study aims to investigate the diagnostic capability of a loop-mediated isothermal amplification (LAMP) assay as an accurate, efficient, and cost-effective alternative to the therascreen assay. Methods EGFR mutations were investigated by LAMP and therascreen assays using tissue samples that were surgically resected or biopsied from 117 consecutive patients with NSCLC tumors. The EGFR status from the LAMP assay was compared with that of the therascreen assay. Next-generation sequencing (NGS) was performed to confirm EGFR status of tumors that did not match in both assays. To establish an optimal LAMP AUC value, receiver operating characteristics (ROC) curve analysis was performed within tumors with exon 19 deletion or L858R point mutation. Results Of the 117 tumors assayed, 45 tumors with EGFR mutations and 68 tumors with EGFR wild type were matched in both assays, four tumors having mismatched EGFR statuses. NGS further confirmed that two of the four discordant tumors had the same EGFR status that was determined by the LAMP assay. The AUC values were 0.973 (95% CI: 0.929–1.00) in exon 19 deletion, and 0.952 (95% CI: 0.885–1.00) in L858R point mutation. In exon 19 deletion, sensitivity, specificity, and accuracy were 89.3%, 98.9%, and 96.6%, respectively, and 94.7%, 95.9%, and 95.7%, respectively, in L858R using AUC value of 0.222. Conclusions The LAMP assay compared favorably with the therascreen assay and has potential as an effective, simple, rapid, and low-cost diagnostic alternative. Based on these results, a liquid biopsy LAMP system should be developed for point-of-care testing of oncogenes in the near future.
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Affiliation(s)
- Yuichi Saito
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan.,Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Nobumasa Takahashi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Atsuka Matsui
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Tochigi, Japan
| | - Satoru Michiyuki
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Tochigi, Japan
| | - Yoshikane Yamauchi
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Yoshihiko Shimizu
- Department of Pathology, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Eishin Hoshi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Yukinori Sakao
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Masafumi Kawamura
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
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Kim J, Park BG, Lim DH, Jang WS, Nam J, Mihn DC, Lim CS. Development and evaluation of a multiplex loop-mediated isothermal amplification (LAMP) assay for differentiation of Mycobacterium tuberculosis and non-tuberculosis mycobacterium in clinical samples. PLoS One 2021; 16:e0244753. [PMID: 33406154 PMCID: PMC7787462 DOI: 10.1371/journal.pone.0244753] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/15/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The rapid and accurate diagnosis of tuberculosis (TB) is important to reduce morbidity and mortality rates and risk of transmission. Therefore, molecular detection methods such as a real-time PCR-based assay for Mycobacterium tuberculosis (MTB) have been commonly used for diagnosis of TB. Loop-mediated isothermal amplification (LAMP) assay was believed to be a simple, quick, and cost-effective isothermal nucleic acid amplification diagnostic test for infectious diseases. In this study, we designed an in-house multiplex LAMP assay for the differential detection of MTB and non-tuberculosis mycobacterium (NTM), and evaluated the assay using clinical samples. MATERIAL AND METHODS For the multiplex LAMP assay, two sets of specific primers were designed: the first one was specific for IS6110 genes of MTB, and the second one was universal for rpoB genes of mycobacterium species including NTM. MTB was confirmed with a positive reaction with both primer sets, and NTM was identified with a positive reaction by only the second primer set without a MTB-specific reaction. Total 333 clinical samples were analyzed to evaluate the multiplex LAMP assay. Clinical samples were composed of 195 positive samples (72 MTB and 123NTM) and 138 negative samples. All samples were confirmed positivity or negativity by real-time PCR for MTB and NTM. Analytical sensitivity and specificity were evaluated for the multiplex LAMP assay in comparison with acid fast bacilli staining and the culture method. RESULTS Of 123 NTM samples, 121 were identified as NTM and 72/72 MTB were identified as MTB by the multiplex LAMP assay. False negative reactions were seen only in two NTM positive samples with co-infection of Candida spp. All 138 negative samples were identified as negative for MTB and NTM. Analytical sensitivity of the multiplex LAMP assay was 100% (72/72) for MTB, and 98.4% (121/123) for NTM. And the specificity of assay was 100% (138/138) for all. CONCLUSIONS Our newly designed multiplex LAMP assay for MTB and NTM showed relatively good sensitivity in comparison with previously published data to detect isolated MTB. This multiplex LAMP assay is expected to become a useful tool for detecting and differentiating MTB from NTM rapidly at an acceptable sensitivity.
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Affiliation(s)
- Jeeyong Kim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Borae G. Park
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Da Hye Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Woong Sik Jang
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Do-CiC Mihn
- Department of Diagnostic Immunology, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
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28
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Aman R, Mahas A, Marsic T, Hassan N, Mahfouz MM. Efficient, Rapid, and Sensitive Detection of Plant RNA Viruses With One-Pot RT-RPA-CRISPR/Cas12a Assay. Front Microbiol 2020; 11:610872. [PMID: 33391239 PMCID: PMC7773598 DOI: 10.3389/fmicb.2020.610872] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/30/2020] [Indexed: 12/25/2022] Open
Abstract
Most viruses that infect plants use RNA to carry their genomic information; timely and robust detection methods are crucial for efficient control of these diverse pathogens. The RNA viruses, potexvirus (Potexvirus, family Alphaflexiviridae), potyvirus (Potyvirus, family Potyviridae), and tobamovirus (Tobamovirus, family Virgaviridae) are among the most economically damaging pathogenic plant viruses, as they are highly infectious and distributed worldwide. Their infection of crop plants, alone or together with other viruses, causes severe yield losses. Isothermal nucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and others have been harnessed for the detection of DNA- and RNA-based viruses. However, they have a high rate of non-specific amplification and other drawbacks. The collateral activities of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease Cas systems such as Cas12 and Cas14 (which act on ssDNA) and Cas13 (which acts on ssRNA) have recently been exploited to develop highly sensitive, specific, and rapid detection platforms. Here, we report the development of a simple, rapid, and efficient RT- RPA method, coupled with a CRISPR/Cas12a-based one-step detection assay, to detect plant RNA viruses. This diagnostic method can be performed at a single temperature in less than 30 min and integrated with an inexpensive commercially available fluorescence visualizer to facilitate rapid, in-field diagnosis of plant RNA viruses. Our developed assay provides an efficient and robust detection platform to accelerate plant pathogen detection and fast-track containment strategies.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Norhan Hassan
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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29
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Ali Z, Aman R, Mahas A, Rao GS, Tehseen M, Marsic T, Salunke R, Subudhi AK, Hala SM, Hamdan SM, Pain A, Alofi FS, Alsomali A, Hashem AM, Khogeer A, Almontashiri NAM, Abedalthagafi M, Hassan N, Mahfouz MM. iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Res 2020; 288:198129. [PMID: 32822689 PMCID: PMC7434412 DOI: 10.1016/j.virusres.2020.198129] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/26/2022]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Rahul Salunke
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Amit K Subudhi
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sharif M Hala
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; King Abdullah International Medical Research Centre - Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fadwa S Alofi
- Infectious Diseases Department, King Fahad Hospital, Madinah, Saudi Arabia
| | - Afrah Alsomali
- King Abdullah Medical Complex (KAMC), Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asim Khogeer
- Plan and Research Department, General Directorate of Health Affairs Makkah Region, MOH, Saudi Arabia
| | - Naif A M Almontashiri
- College of Applied Medical Sciences and Center for Genetics and Inherited Diseases, Taibah University, Madinah, Saudi Arabia
| | - Malak Abedalthagafi
- King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Norhan Hassan
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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Pragmatic accuracy of an in-house loop-mediated isothermal amplification (LAMP) for diagnosis of pulmonary tuberculosis in a Thai community hospital. PLoS One 2020; 15:e0236496. [PMID: 32702008 PMCID: PMC7377475 DOI: 10.1371/journal.pone.0236496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND To improve the quality of diagnosing pulmonary tuberculosis (TB), WHO recommends the use of rapid molecular testing as an alternative to conventional microscopic methods. Loop-mediated isothermal amplification assay (LAMP test) is a practical and cost-effective nucleic amplification technique. We evaluated the pragmatic accuracy of an in-house LAMP assay for the diagnosis of TB in a remote health care setting where an advanced rapid molecular test is not available. METHODS A prospective diagnostic accuracy study was conducted. Patients with clinical symptoms suggestive of TB were consecutively enrolled from April to August 2016. Sputum samples were collected from each patient and were sent for microscopic examination (both acid-fast stain and fluorescence stain), in-house LAMP test, and TB culture. RESULTS One hundred and seven patients with TB symptoms were used in the final analysis. This included 50 (46.7%) culture-positive TB patients and 57 (53.3%) culture-negative patients. The overall sensitivity of the in-house LAMP based on culture positivity was 88.8% (95/107) with a 95%CI of 81.2-94.1. The sensitivity was 90.9% (40/44) with a 95%CI of 78.3-97.5 for smear-positive, culture-positive patients, and was 16.7% (1/6) with a 95%CI of 0.4-64.1 for smear-negative, culture-positive patients. The overall sensitivity of the in-house LAMP test compared to smear microscopy methods were not significantly different (p = 0.375). The specificity of the in-house LAMP based on non-TB patients (smear-negative, culture-negative) was 94.7% (54/57) with a 95%CI of 85.4-98.9. CONCLUSIONS The diagnostic accuracy of the in-house LAMP test in a community hospital was comparable to other previous reports in terms of specificity. The sensitivity of the in-house assay could be improved with better sputum processing and DNA extraction method.
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Phetsuksiri B, Klayut W, Rudeeaneksin J, Srisungngam S, Bunchoo S, Toonkomdang S, Wongchai T, Nakajima C, Suzuki Y. The performance of an in-house loop-mediated isothermal amplification for the rapid detection of Mycobacterium tuberculosis in sputum samples in comparison with Xpert MTB/RIF, microscopy and culture. Rev Inst Med Trop Sao Paulo 2020; 62:e36. [PMID: 32520211 PMCID: PMC7274762 DOI: 10.1590/s1678-9946202062036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022] Open
Abstract
Simple, low-cost and effective diagnostic tests for tuberculosis (TB) are needed especially in TB-high burden settings. The present study evaluated the performance of an in-house loop-mediated isothermal amplification (LAMP) for diagnosing TB by comparing it to Xpert MTB/RIF, microscopy and culture. In Thailand, a total of 204 excess sputum samples volume after the processing of cultures were used for Mycobacterium tuberculosis (MTB) detection by Xpert MTB/RIF and LAMP. Based on culture results as the gold standard, the overall sensitivity of LAMP and Xpert MTB/RIF were 82.1% (126/153; 95% confidential interval [CI]: 75.4-88.98%) and 86.9 % (133/153; 95% CI: 80.5-90.8%) respectively, and the specificity of both tests was 100% (51/51; 95% CI: 93.0-100.0%). In comparison with Xpert MTB/RIF, the sensitivity and specificity of LAMP were 94.7% (126/133; 95% CI: 89.5-97.9%), and 100.0% (73/73; 95% CI: 94.9-100.0%), respectively. The average threshold cycle (Ct) of Xpert MTB/RIF detection for positive and negative LAMP results was statistically different, of 18.4 and 27.0, respectively (p < 0.05). In comparison with the acid-fast staining technique, and analyzing LAMP and Xpert MTB/RIF in smear-negative/culture-positive specimens, there was an increase of the detection rate by 47.7% (21/44) and 54.6% (24/44). The diagnostic sensitivity and specificity of LAMP appeared to be comparable to those of Xpert MTB/RIF. We claim that this LAMP has potential to provide a sensitive diagnostic test for the rapid TB diagnosis. It allowed a fast detection of MTB before the cultures and it could be used in resource-limited laboratory settings.
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Affiliation(s)
- Benjawan Phetsuksiri
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Wiphat Klayut
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Janisara Rudeeaneksin
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sopa Srisungngam
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Supranee Bunchoo
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | | | - Thanee Wongchai
- Mae Sot Hospital, Department of Medical Technology, Tak, Thailand
| | - Chie Nakajima
- Hokkaido University, Research Center for Zoonosis Control, Division of Bioresources, Sapporo, Japan.,Hokkaido University, Global Institution for Collaborative Research and Education, Global Station for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Hokkaido University, Research Center for Zoonosis Control, Division of Bioresources, Sapporo, Japan.,Hokkaido University, Global Institution for Collaborative Research and Education, Global Station for Zoonosis Control, Sapporo, Japan
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32
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Combining the Sensitivity of LAMP and Simplicity of Primer Extension via a DNA-Modified Nucleotide. CHEMISTRY 2020. [DOI: 10.3390/chemistry2020029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
LAMP is an approach for isothermal nucleic acids diagnostics with increasing importance but suffers from the need of tedious systems design and optimization for every new target. Here, we describe an approach for its simplification based on a single nucleoside-5′-O-triphosphate (dNTP) that is covalently modified with a DNA strand. We found that the DNA-modified dNTP is a substrate for DNA polymerases in versatile primer extension reactions despite its size and that the incorporated DNA indeed serves as a target for selective LAMP analysis.
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Peláez EC, Estevez MC, Mongui A, Menéndez MC, Toro C, Herrera-Sandoval OL, Robledo J, García MJ, Portillo PD, Lechuga LM. Detection and Quantification of HspX Antigen in Sputum Samples Using Plasmonic Biosensing: Toward a Real Point-of-Care (POC) for Tuberculosis Diagnosis. ACS Infect Dis 2020; 6:1110-1120. [PMID: 32233503 DOI: 10.1021/acsinfecdis.9b00502] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Advancements that occurred during the last years in the diagnosis of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis infection, have prompted increased survival rates of patients. However, limitations related to the inefficiency of an early detection still remain; some techniques and laboratory methods do not have enough specificity and most instruments are expensive and require handling by trained staff. In order to contribute to a prompt and effective diagnosis of tuberculosis, we report the development of a portable, user-friendly, and low-cost biosensor device for its early detection. By using a label-free surface plasmon resonance (SPR) biosensor, we have established a direct immunoassay for the direct detection and quantification of the heat shock protein X (HspX) of Mtb, a well-established biomarker of this pathogen, directly in pretreated sputum samples. The method relies on highly specific monoclonal antibodies that are previously immobilized on the plasmonic sensor surface. This technology allows for the direct detection of the biomarker without amplification steps, showing a limit of detection (LOD) of 0.63 ng mL-1 and a limit of quantification (LOQ) of 2.12 ng mL-1. The direct analysis in pretreated sputum shows significant differences in the HspX concentration in patients with tuberculosis (with concentration levels in the order of 116-175 ng mL-1) compared with non-tuberculosis infected patients (values below the LOQ of the assay).
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Affiliation(s)
- Enelia Cristina Peláez
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER-BBN and BIST, Campus UAB, 08193 Barcelona, Spain
- Centro de Investigación y Desarrollo Tecnológico de la Industria Electro Electrónica y TIC (CIDEI), Calle 45a BIS # 19-09 Floor 2, Bogotá, DC, Colombia
- Corporación CorpoGen, Departamento Biotecnología Molecular, Carrera 4 # 20-41, Bogotá, DC, Colombia
- Research Cluster on Converging Sciences and Technology (NBIC), Universidad Central, Calle 21 #4-40, Bogotá, DC, Colombia
| | - Maria Carmen Estevez
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER-BBN and BIST, Campus UAB, 08193 Barcelona, Spain
| | - Alvaro Mongui
- Corporación CorpoGen, Departamento Biotecnología Molecular, Carrera 4 # 20-41, Bogotá, DC, Colombia
| | - M-Carmen Menéndez
- Departamento de Medicina Preventiva, Salud Pública y Microbiología, Facultad de Medicina, Universidad Autónoma de Madrid, St Arzobispo Morcillo s/n, 28029 Madrid, Spain
| | - Carlos Toro
- Department of Microbiology, La Paz University Hospital, IdiPaz, St/Paseo de la Castellana 261, 28046 Madrid, Spain
| | - Oscar L. Herrera-Sandoval
- Centro de Investigación y Desarrollo Tecnológico de la Industria Electro Electrónica y TIC (CIDEI), Calle 45a BIS # 19-09 Floor 2, Bogotá, DC, Colombia
- Research Cluster on Converging Sciences and Technology (NBIC), Universidad Central, Calle 21 #4-40, Bogotá, DC, Colombia
| | - Jaime Robledo
- Corporación para Investigaciones Biológicas (CIB), Laboratorio de Micobacterias, Carrera 72A 78B-141, 050034 Medellín, Colombia
| | - Maria J. García
- Departamento de Medicina Preventiva, Salud Pública y Microbiología, Facultad de Medicina, Universidad Autónoma de Madrid, St Arzobispo Morcillo s/n, 28029 Madrid, Spain
| | - Patricia Del Portillo
- Corporación CorpoGen, Departamento Biotecnología Molecular, Carrera 4 # 20-41, Bogotá, DC, Colombia
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, CIBER-BBN and BIST, Campus UAB, 08193 Barcelona, Spain
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Phetsuksiri B, Rudeeaneksin J, Srisungngam S, Bunchoo S, Klayut W, Nakajima C, Hamada S, Suzuki Y. Comparison of Loop-Mediated Isothermal Amplification, Microscopy, Culture, and PCR for Diagnosis of Pulmonary Tuberculosis. Jpn J Infect Dis 2020; 73:272-277. [PMID: 32115540 DOI: 10.7883/yoken.jjid.2019.335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The diagnosis of tuberculosis (TB) in endemic countries is challenging due to high caseloads and limited resources. A simple and cost-effective diagnostic test for the rapid detection of Mycobacterium tuberculosis (M. tuberculosis) in clinical specimens is crucially needed. We evaluated the performance of an in-house assay based on loop-mediated isothermal amplification (LAMP) targeting the M. tuberculosis 16S ribosomal RNA (rRNA) gene for the diagnosis of TB in Thailand. A total of 252 sputum samples from suspected cases of pulmonary TB were analyzed. The sensitivity of LAMP was 99.04% (103/104; 95% confidence interval [CI]: 94.76-9.98%) and 72.73% (16/22; 95% CI: 49.78-89.27%) for smear-positive and smear-negative samples with TB-culture positivity, respectively. LAMP detected 20.69% (24/116) of TB culture negative samples but all those were positive by conventional polymerase chain reaction (PCR). The sensitivity of LAMP was higher than that of sputum microscopy while the performance of LAMP was similar to PCR. None of the samples positive for non-tuberculous mycobacteria by culture and PCR were positive by LAMP. Compared to TB culture, the positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient of LAMP were 83.22%, 88.33%, and 0.75 respectively. Based on the diagnostic performance, we propose that LAMP would be suitable as a potential diagnostic test for rapid TB diagnosis in resource-limited laboratory settings.
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Affiliation(s)
- Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Wiphat Klayut
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Japan
| | - Shigeyuki Hamada
- Section of Bacterial Infections, Research Collaboration Center for Emerging and Re-emerging Infectious Diseases, Thailand.,Research Institute for Microbial Diseases, Osaka University, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Japan
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Wei Z, Zhang X, Wei C, Yao L, Li Y, Zhang X, Xu H, Jia Y, Guo R, Wu Y, Yang K, Gao X. Diagnostic accuracy of in-house real-time PCR assay for Mycobacterium tuberculosis: a systematic review and meta-analysis. BMC Infect Dis 2019; 19:701. [PMID: 31395014 PMCID: PMC6686366 DOI: 10.1186/s12879-019-4273-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 07/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, studies on the diagnostic accuracy of in-house real-time PCR (hRT-PCR) assay for the detection of Mycobacterium tuberculosis (Mtb) have been reported with unignorable discrepancies. To assess the overall accuracy of the hRT-PCR assay for Mtb diagnosis in different samples for individuals with active pulmonary and extra-pulmonary Mtb infection, a systematic review and meta-analysis were performed. METHODS The PUBMED, EMBASE, Web of Science, and Cochrane databases were searched up to June 2017 for eligible studies that estimated diagnostic sensitivity and specificity with the hRT-PCR assay in respiratory and non-respiratory samples in pulmonary and extra-pulmonary Mtb infection patients, with Mtb culture as the reference standard. Bivariate random effect models were used to provide pooled estimation of diagnostic accuracy. Further, subgroup and meta-regression analyses were performed to explore sources of heterogeneity. The risk of bias was assessed by the QUADAS-2 tool. RESULTS Of the 3589 candidate studies, 18 eligible studies met our inclusion criteria. Compared to Mtb culture data, the pooled sensitivity and specificity were 0.96 and 0.92, respectively. The diagnostic odds ratio (DOR) was 192.96 (95% CI 68.46, 543.90), and the area under the summary ROC curve (AUC) was 0.9791. There was significant heterogeneity in sensitivity and specificity among the enrolled studies (p < 0.001). The studies with high-quality assessment and application of respiratory specimen were associated with better accuracy. CONCLUSIONS In low-income/high-burden settings, our results suggested that the hRT-PCR assay could be a useful test for the diagnosis of TB with high sensitivity and specificity.
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Affiliation(s)
- Zhenhong Wei
- Blood Transfusion Department, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China
| | - Xiaoping Zhang
- Blood Transfusion Department, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China
| | - Chaojun Wei
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Liang Yao
- The Institute of Clinical Study and Evidence-Based Medicine, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China.,Evidence-Based Medicine Center and Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, College of Basic Medicine, Lanzhou University, No. 199, Donggang street, Chengguan district, Lanzhou, 73000, Gansu, China
| | - Yonghong Li
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Xiaojing Zhang
- Blood Transfusion Department, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China
| | - Hui Xu
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Yanjuan Jia
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Rui Guo
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Yu Wu
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China
| | - Kehu Yang
- The Institute of Clinical Study and Evidence-Based Medicine, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China. .,Evidence-Based Medicine Center and Key Laboratory of Evidence-Based Medicine and Knowledge Translation of Gansu Province, College of Basic Medicine, Lanzhou University, No. 199, Donggang street, Chengguan district, Lanzhou, 73000, Gansu, China.
| | - Xiaoling Gao
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, No. 204, Donggang street, Chengguan district, Lanzhou, 730000, Gansu, China.
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Rakotosamimanana N, Lapierre SG, Raharimanga V, Raherison MS, Knoblauch AM, Raherinandrasana AH, Rakotoson A, Rakotonirina J, Rasolofo V. Performance and impact of GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® assays on tuberculosis case detection in Madagascar. BMC Infect Dis 2019; 19:542. [PMID: 31221109 PMCID: PMC6585144 DOI: 10.1186/s12879-019-4198-6] [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] [Received: 04/12/2019] [Accepted: 06/16/2019] [Indexed: 12/02/2022] Open
Abstract
Background Tuberculosis rapid molecular assays, including GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit®, are highly sensitive and specific. Such performance does not automatically translate in improved disease control and highly depends on their use, local epidemiology and the diagnostic algorithms they’re implemented within. We evaluate the performance of both assays and assess their impact on additional cases notification when implemented within WHO recommended tuberculosis diagnostic algorithms in Madagascar. Methods Five hundred forty eight presumptive pulmonary tuberculosis patients were prospectively recruited between November 2013 and December 2014 in Antananarivo, Madagascar, a high TB incidence sub-Saharan African urban setting. Both molecular assays were evaluated as first line or add-on testing following negative smear microscopy. Based on locally defined assay performance characteristics we measure the impact of both assays and WHO-recommended diagnostic algorithms on additional tuberculosis case notifications. Results High sensitivity and specificity was confirmed for both GeneXpert MTB/RIF® (86.6% (95% CI 81.1–90.7%) and 97.4% (95% CI 94.9–98.8%)) and Loopamp MTBC Detection Kit® (84.6% (95% CI 78.9–89.0%) and 98.4% (95% CI 96.2–99.4%)). Implementation of GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® increased tuberculosis diagnostic algorithms sensitivity from 73.6% (95% CI 67.1–79.3%) up to 88.1% (95% CI 82.8–91.9%). This increase was highest when molecular assays were used as add-on testing following negative smear microscopy. As add-on testing, GeneXpert MTB/RIF® and Loopamp MTBC Detection Kit® respectively improved case detection by 23.8 and 21.2% (p < 0.05). Conclusion Including GeneXpert MTB/RIF® or Loopamp MTBC Detection Kit® molecular assays for TB detection on sputum samples from presumptive TB cases can significantly increase case notification in TB diagnostic centers. The TB case detection rate is further increased when those tests are use as second-line follow-on testing following negative smear microscopy results. A country wide scale-up and digital integration of molecular-based TB diagnosis assays shows promises for TB control in Madagascar.
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Affiliation(s)
| | - Simon Grandjean Lapierre
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Immunopathology axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Canada
| | | | - Mamy Serge Raherison
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Service du Laboratoire des Mycobactéries, Ministry of Public Health, Antananarivo, Madagascar
| | - Astrid M Knoblauch
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Epidemiology and Public Health Department, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Andrianantenaina Rakotoson
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,Epidemiology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Julio Rakotonirina
- Centre hospitalier universitaire de soins et de santé publique d'Analakely, Analakely, Antananarivo, Madagascar
| | - Voahangy Rasolofo
- Mycobacteria Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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Thapa J, Maharjan B, Malla M, Fukushima Y, Poudel A, Pandey BD, Hyashida K, Gordon SV, Nakajima C, Suzuki Y. Direct detection of Mycobacterium tuberculosis in clinical samples by a dry methyl green loop-mediated isothermal amplification (LAMP) method. Tuberculosis (Edinb) 2019; 117:1-6. [PMID: 31378262 DOI: 10.1016/j.tube.2019.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/09/2019] [Accepted: 05/19/2019] [Indexed: 11/19/2022]
Abstract
The purpose of this study was to develop a simple visual methyl green (MeG) based dry loop-mediated isothermal amplification (LAMP) method for early detection of Mycobacterium tuberculosis (MTB) from clinical samples. We identified MeG as an indicator of a positive LAMP reaction, where a positive reaction gave a blue-green color while a negative reaction was colorless. The MeG MTB-LAMP system was further simplified by drying all reagents for ease of use, and was then validated for its ability to diagnose TB directly using Nepalese clinical samples. We evaluated the dry MeG MTB-LAMP with 69 new TB suspected samples from patients that did not have a confirmed history of TB treatment and found the sensitivity in culture positive samples as 92.8% (13/14) and specificity in culture negative samples as 96.3% (53/55). Our LAMP system has the potential to be a point of care test for early diagnosis of active TB in developing countries.
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Affiliation(s)
- Jeewan Thapa
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Hokkaido University, Kita-12 Nishi-5, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
| | - Bhagwan Maharjan
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan; German Nepal Tuberculosis Project, Kalimati, Kathmandu, Nepal; Healthy Nepal, Balkhu, Kathmandu, Nepal
| | - Meena Malla
- Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Ajay Poudel
- Department of Microbiology, Chitwan Medical College Teaching Hospital, Chitwan, Nepal
| | | | - Kyoko Hyashida
- Division of Collaboration and Education, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, D04 W6F6, Ireland; The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan; The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Kita 20 Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0020, Japan; The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan.
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Yoshida S, Suga S, Ishikawa S, Mukai Y, Tsuyuguchi K, Inoue Y, Yamamoto T, Wada T. Mycobacterium caprae Infection in Captive Borneo Elephant, Japan. Emerg Infect Dis 2019; 24:1937-1940. [PMID: 30226170 PMCID: PMC6154153 DOI: 10.3201/eid2410.180018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In 2016, disseminated tuberculosis caused by Mycobacterium caprae was diagnosed in a captive Borneo elephant in Japan. The bacterium was initially identified from clinical isolates. An isolate collected during a relapse showed isoniazid monoresistance and a codon 315 katG mutation.
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Koch HR, Blohm‐Sievers E, Liedvogel M. Rapid sex determination of a wild passerine species using loop-mediated isothermal amplification (LAMP). Ecol Evol 2019; 9:5849-5858. [PMID: 31161003 PMCID: PMC6540700 DOI: 10.1002/ece3.5168] [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] [Received: 10/17/2018] [Revised: 03/14/2019] [Accepted: 03/22/2019] [Indexed: 02/04/2023] Open
Abstract
Many bird species are sexually monomorphic and cannot be sexed based on phenotypic traits. Rapid sex determination is often a necessary component of avian studies focusing on behavior, ecology, evolution, and conservation. While PCR-based methods are the most common technique for molecularly sexing birds in the laboratory, a simpler, faster, and cheaper method has emerged, which can be used in the laboratory, but importantly also in the field. Herein, we used loop-mediated isothermal amplification (LAMP) for rapid sex determination of blood samples from juvenile European blackcaps, Sylvia atricapilla, sampled in the wild. We designed LAMP primers unique to S. atricapilla based on the sex chromosome-specific gene, chromo-helicase-DNA-binding protein (CHD), optimized the primers for laboratory and field application, and then used them to test a subset of wild-caught juvenile blackcaps of unknown gender at the time of capture. Sex determination results were fast and accurate. The advantages of this technique are that it allows researchers to identify the sex of individual birds within hours of sampling and eliminates the need for direct access to a laboratory if implemented at a remote field site. This work adds to the increasing list of available LAMP primers for different bird species and is a new addition within the Passeriformes order.
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Affiliation(s)
- Hanna R. Koch
- Max Planck Research Group Behavioral GenomicsMax Planck Institute for Evolutionary BiologyPlönGermany
| | - Elke Blohm‐Sievers
- Max Planck Research Group Behavioral GenomicsMax Planck Institute for Evolutionary BiologyPlönGermany
| | - Miriam Liedvogel
- Max Planck Research Group Behavioral GenomicsMax Planck Institute for Evolutionary BiologyPlönGermany
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Filipenko ML, Oscorbin IP, Khrapov EA, Shamovskaya DA, Cherednichenko AG, Shvartz Y. Detection of Ser450Leu mutation in rpoB gene of Mycobacterium tuberculosis by allele-specific loop-mediated isothermal DNA amplification method. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To identify genetic mutations a rather time-consuming and expensive method of polymerase chain reaction (PCR) is widely used. The aim of the present work was to evaluate the possibility of using the two schemes of the method of allele-specific isothermal loop amplification (LAMP) to detect the TCG/TTG (S450L) mutation in the rpoB gene of Mycobacterium tuberculosis. 48 clinical isolates of M. tuberculosis and 11 samples of sputum were used, randomized and obtained in the microbiological laboratory of the city of Novosibirsk from incident patients. It is shown that the use of an analysis scheme using the allele-specific primer FIP compared to F3 has the best resolution: the difference between the amplification time of the mutation and the wild type allele was 22 ± 2,4 versus 13 ± 4,1 minutes (p = 0,0011). When using 100 DNA genomic equivalents a true positive signal (amplification of the rpoB gene with a mutation using the corresponding allele-specific primer) was detected after 29,4 ± 3,4 minutes. A positive signal was visualized after adding SYBR Green I to the reaction, both when illuminated with daylight and when using a UV transilluminator. Using the developed method the DNA sample of 20 RIFR isolates from M. tuberculosis was analyzed containing the Ser450Leu mutation in the rpoB gene, 10 RIFR isolates containing other mutations in the rpoB gene and 18 RIFs isolates without any mutations; the presence of mutations in the samples was determined using classical Sanger sequencing. The sensitivity and specificity of LAMP for detecting a Ser450Leu mutation in the rpoB gene was 100%. This approach allows the use of crude lysates of mycobacteria as DNA, which reduces the total analysis time to 1,5 hour.
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Affiliation(s)
- ML Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - IP Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - EA Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - DA Shamovskaya
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | | | - YaSh Shvartz
- Novosibirsk Tuberculosis Research Institute, Novosibirsk, Russia
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Accuracy of Commercial Molecular Diagnostics for the Detection of Pulmonary Tuberculosis in China: A Systematic Review. Sci Rep 2019; 9:4553. [PMID: 30872692 PMCID: PMC6418248 DOI: 10.1038/s41598-019-41074-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 02/28/2019] [Indexed: 12/14/2022] Open
Abstract
This systematic review assesses the accuracy of molecular diagnostic methods for the detection of pulmonary tuberculosis in studies performed in China, published in Chinese and English. We searched for studies that assessed the accuracy of molecular diagnostics for pulmonary TB in China in the China National Knowledge Infrastructure, the Wanfang Database, SinoMed, VIP Information, Pubmed, Embase, and the Cochrane Library. For each index test, a summary estimation for sensitivity and specificity was calculated using the bivariate random-effects model. A total of 59 studies were included in our analysis. Loop-mediated isothermal amplifcation (LAMP) assay (six studies; pooled sensitivity 90%, 95% CI 78-95%; specificity 93%, 85-97%), line probe assay (LPA) (one study; 87%, 84-90%; 94%, 92-95%) and polymerase chain reaction (PCR) (FQ-PCR and RT-PCR) (four studies; 90%, 55-99%; 93%, 71-99%) showed good diagnostic performance in the meta-analysis. The highest pooled sensitivity was from Xpert MTB/RIF (20 studies; pooled sensitivity 91%, 95% CI 87-94%). The highest pooled specificity was from cross-priming amplification (CPA) (six studies; pooled specificity 97%, 95-99%). The lowest pooled sensitivity and specificity were from simultaneous amplification and testing (SAT)-TB (three studies; 79%, 66-88%; 72%, 48-88%). In subgroup analysis, molecular diagnostics demonstrated higher sensitivity for pulmonary TB detection in smear-positive specimens. Xpert MTB/RIF, LAMP, LPA, CPA and PCR demonstrated high accuracy overall for pulmonary tuberculosis detection, while SAT-TB had poor performance.
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Joon D, Nimesh M, Gupta S, Kumar C, Varma-Basil M, Saluja D. Development and evaluation of rapid and specific sdaA LAMP-LFD assay with Xpert MTB/RIF assay for diagnosis of tuberculosis. J Microbiol Methods 2019; 159:161-166. [PMID: 30858005 DOI: 10.1016/j.mimet.2019.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 11/19/2022]
Abstract
There is need for rapid and cost-effective diagnostic test for tuberculosis. The present study was carried out to design a Loop-mediated isothermal amplification (LAMP) assay combined with lateral flow dipstick (LFD) as a point-of-care method for diagnosis of TB. LAMP assay targeting sdaA gene combined with LFD for sequence specific detection was standardized in user friendly and rapid format. It does not require sophisticated instruments and shows visual results instantly. The LAMP-LFD assay was validated using culture confirmed specimens. The assay was evaluated in a cross-sectional study using respiratory specimens collected from patients in Delhi, India and it showed high concordance with GeneXpert MTB/RIF assay. Lateral flow dipstick method has provided an excellent detection format with LAMP method. The LAMP-LFD assay showed high diagnostic accuracy in comparison to other methods and can be used as a point-of-care test in cost-effective manner.
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Affiliation(s)
- Deepali Joon
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India; Shri Guru Tegh Bahadur Khalsa College, University of Delhi, Delhi 110 007, India
| | - Manoj Nimesh
- Shri Guru Tegh Bahadur Khalsa College, University of Delhi, Delhi 110 007, India
| | - Shraddha Gupta
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 11007, India
| | - Chanchal Kumar
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 11007, India
| | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 11007, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110 007, India.
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MacLean E, Broger T, Yerlikaya S, Fernandez-Carballo BL, Pai M, Denkinger CM. A systematic review of biomarkers to detect active tuberculosis. Nat Microbiol 2019; 4:748-758. [PMID: 30804546 DOI: 10.1038/s41564-019-0380-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 01/18/2019] [Indexed: 12/12/2022]
Abstract
Millions of cases of tuberculosis (TB) go undiagnosed each year. Better diagnostic tools are urgently needed. Biomarker-based or multiple marker biosignature-based tests, ideally performed on blood or urine, for the detection of active TB might help to meet target product profiles proposed by the World Health Organization for point-of-care testing. We conducted a systematic review to summarize evidence on proposed biomarkers and biosignatures and evaluate their quality and level of evidence. We screened the titles and abstracts of 7,631 citations and included 443 publications that fulfilled the inclusion criteria and were published in 2010-2017. The types of biomarkers identified included antibodies, cytokines, metabolic activity markers, mycobacterial antigens and volatile organic compounds. Only 47% of studies reported a culture-based reference standard and diagnostic sensitivity and specificity. Forty-four biomarkers (4%) were identified in high-quality studies and met the target product profile minimum criteria, of which two have been incorporated into commercial assays. Of the 44 highest-quality biomarkers, 24 (55%) were multiple marker biosignatures. No meta-analyses were performed owing to between-study heterogeneity. In conclusion, TB biomarker discovery studies are often poorly designed and findings are rarely confirmed in independent studies. Few markers progress to a further developmental stage. More validation studies that consider the intended diagnostic use cases and apply rigorous design are needed. The extracted data from this review are currently being used by FIND as the foundation of a dynamic database in which biomarker data and developmental status will be presented.
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Affiliation(s)
- Emily MacLean
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Québec, Canada
| | | | | | | | - Madhukar Pai
- McGill International TB Centre, Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
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Rajput R, Singh P, Sarin R, Sethi P, Sharma S. Diagnostic accuracy of loop-mediated isothermal amplification assay for extra-pulmonary tuberculosis in Indian population. J Microbiol Methods 2019; 158:59-65. [PMID: 30703448 DOI: 10.1016/j.mimet.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Confirmatory diagnosis of extra-pulmonary tuberculosis remains a true challenge owing to difficulty in procuring appropriate specimen, inefficient laboratory methods and paucibacillary nature of infection. These obstructions become all the very difficult in pediatric EPTB cases, due to non-specific clinical signs and symptoms, low sensitivity of smear microscopy and culture, lack of awareness among clinicians, etc. AIM OF THE STUDY: The present study aimed to evaluate the diagnostic accuracy of rapid and cost-effective loop-mediated isothermal amplification (LAMP) assay for EPTB diagnosis in children. METHODS A total of 154 cases were analyzed by EPTB-site smear microscopy, culture, PCRs for IS6110, MPB64 & Pab genes, nested PCR and LAMP assay. Single-gene PCRs were performed by custom-synthesized primers. Nested PCR was performed using the 3B BIOTUB Kit and the LAMP assay was done using the Nu-LAMP TB kit. RESULTS We observed that the molecular tests displayed 4-fold higher positivity rate (minimum 46%) in comparison to the microbiological tests (maximum 11.03%). In contrast to the composite reference standard, LAMP assay was found to be 79.6% sensitive and 78% specific for EPTB diagnosis in childhood cases. CONCLUSIONS Our results indicate that LAMP assay is a promising technique for efficient diagnosis of EPTB in children belonging to resource-limited regions.
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Affiliation(s)
- Roopali Rajput
- Department of Molecular Medicine, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Paras Singh
- Department of Molecular Medicine, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India.
| | - Rohit Sarin
- Department of TB and Respiratory Diseases and Director, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Prabhpreet Sethi
- Department of TB and Respiratory Diseases, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
| | - Sangeeta Sharma
- Department of Paediatrics, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi, India
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Machado D, Couto I, Viveiros M. Advances in the molecular diagnosis of tuberculosis: From probes to genomes. INFECTION GENETICS AND EVOLUTION 2018; 72:93-112. [PMID: 30508687 DOI: 10.1016/j.meegid.2018.11.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 11/29/2022]
Abstract
Tuberculosis, disease caused by Mycobacterium tuberculosis, is currently the leading cause of death by a single infectious agent worldwide. Early, rapid and accurate identification of M. tuberculosis and the determination of drug susceptibility is essential for the treatment and management of this disease. Tuberculosis diagnosis is mainly based on chest radiography, smear microscopy and bacteriological culture. Smear microscopy has variable sensitivity, mainly in patients co-infected with the human immunodeficiency virus (HIV). Conventional culture for M. tuberculosis isolation, identification and drug susceptibility testing requires several weeks owning to the slow growth of M. tuberculosis. The delay in the time to results drives the prolongation of potentially inappropriate antituberculosis therapy contributing to the emergence of drug resistance, reducing treatment options and increasing treatment duration and associated costs, resulting in increased mortality and morbidity. For these reasons, novel diagnostic methods are need for timely identification of M. tuberculosis and determination of the antibiotic susceptibility profile of the infecting strain. Molecular methods offer enhanced sensitivity and specificity, early detection and the capacity to detect mixed infections. These technologies have improved turnaround time, cost effectiveness and are amenable for point-of-care testing. However, although these methods produce results within hours from sample collection, the phenotypic susceptibility testing is still needed for the determination of drug susceptibility and quantify the susceptibility levels of a given strain towards individual antibiotics. This review presents the history, advances and forthcoming promises in the molecular diagnosis of tuberculosis. An overview on the general principles, diagnostic value and the main advantages and disadvantages of the molecular methods used for the detection and identification of M. tuberculosis and its associated disease, is provided. It will be also discussed how the current phenotypic methods should be used in combination with the genotypic methods for rapid antituberculosis susceptibility testing.
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Affiliation(s)
- Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Isabel Couto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal.
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Grandjean Lapierre S, Drancourt M. rpoB Targeted Loop-Mediated Isothermal Amplification (LAMP) Assay for Consensus Detection of Mycobacteria Associated With Pulmonary Infections. Front Med (Lausanne) 2018; 5:332. [PMID: 30547031 PMCID: PMC6279915 DOI: 10.3389/fmed.2018.00332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/12/2018] [Indexed: 11/30/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid method which has been used to identify mycobacteria including Mycobacterium tuberculosis in clinical microbiology laboratory and point of care settings. Previously published LAMP protocols for detection of mycobacterial species used conventional specific primer and targeted the 16S rRNA, gyrB, and insertion sequence genes. We developed and evaluated a LAMP assay targeting a mycobacterial rpoB gene conserved sequence and incorporating degenerate primers. This assay allowed consensus detection of mycobacterial species from pure culture, clinical respiratory tract samples, and mycobacteria growth indicator tube (MGIT) liquid-based culture medium. A panel of twenty mycobacterial species were successfully detected at detection thresholds of 102 CFU/mL and 103 CFU/mL when respectively performed on pure culture suspension or sputum and MGIT broth. The inclusion of degenerate bases in LAMP primers increased the diversity of mycobacterial species identified by the assay without negatively affecting analytical sensitivity. LAMP-based consensus detection of multiple pathogens can be achieved with degenerate primers therefore allowing the design of rapid multi-disease screening assays. Despite high analytical sensitivity, species specificity and the advantageous operational characteristics of LAMP over PCR, challenges such as potential ambiguity in visual interpretation of results and occasional non-specific amplification precludes the implementation of novel LAMP assay in routine diagnostics both in centralized and point-of-care laboratory.
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Affiliation(s)
- Simon Grandjean Lapierre
- Aix-Marseille Université, IRD 198, MEPHI, IHU Méditerranée Infection, Marseille, France
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Michel Drancourt
- Aix-Marseille Université, IRD 198, MEPHI, IHU Méditerranée Infection, Marseille, France
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Kim CK, Cho EA, Shin DM, Choi SW, Shin SY. Comparative Evaluation of the Loop-Mediated Isothermal Amplification Assay for Detecting Pulmonary Tuberculosis. Ann Lab Med 2018; 38:119-124. [PMID: 29214755 PMCID: PMC5736670 DOI: 10.3343/alm.2018.38.2.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 07/07/2017] [Accepted: 10/10/2017] [Indexed: 11/19/2022] Open
Abstract
Background Early detection of tuberculosis (TB) is challenging in resource-poor settings because of limited accessibility to molecular diagnostics. The aim of this study was to evaluate the performance of the loop-mediated isothermal amplification kit (TB-LAMP) for TB diagnosis compared with conventional and molecular tests. Methods A total of 290 consecutive sputum samples were collected from May till September, 2015. All samples were processed using the N-Acetyl-L-cysteine (NALC) NaOH method and tested by smear microscopy, solid and liquid culture, real-time PCR, and TB-LAMP. Results The sensitivity of TB-LAMP for smear-positive and smear-negative samples with culture positivity was 92.0% and 58.8%, respectively. TB-LAMP was positive in 14.9% of TB culture-negative samples; however, all those samples were also positive by real-time PCR. In addition, none of the samples positive for nontuberculous mycobacteria by culture were positive by TB-LAMP. The overall agreement between TB-LAMP and real-time PCR was good; however, the concordance rate was significantly lower for real-time PCR positive samples with Ct values of 30–35. Conclusions TB-LAMP could replace smear microscopy and increase TB diagnostic capacity when Xpert MTB/RIF is not feasible because of poor infrastructure.
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Affiliation(s)
- Chang Ki Kim
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Guri, Korea.
| | - Eun A Cho
- Korean Institute of Tuberculosis, Cheongju, Korea
| | - Dong Mi Shin
- Korean Institute of Tuberculosis, Cheongju, Korea
| | | | - So Youn Shin
- Korean Institute of Tuberculosis, Cheongju, Korea
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Yu G, Shen Y, Zhong F, Ye B, Yang J, Chen G. Diagnostic accuracy of the loop-mediated isothermal amplification assay for extrapulmonary tuberculosis: A meta-analysis. PLoS One 2018; 13:e0199290. [PMID: 29944682 PMCID: PMC6019099 DOI: 10.1371/journal.pone.0199290] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/05/2018] [Indexed: 01/26/2023] Open
Abstract
Background Loop-mediated isothermal amplification (LAMP) is used to detect pulmonary tuberculosis (PTB); however, the diagnostic accuracy of the LAMP assay for extrapulmonary tuberculosis (EPTB) is unclear. We performed a meta-analysis to evaluate the performance of LAMP in the detection of EPTB. Methods We searched PubMed, EMBASE, the Cochrane Library, China National Knowledge Infrastructure (CNKI), and the Wanfang database for studies published before Sep 16, 2017. We reviewed studies and compared the performance of LAMP with that of a composite reference standard (CRS) and culture for clinically suspected EPTB. We used a bivariate random-effects model to perform meta-analyses and used meta-regression and subgroup analysis to analyze sources of heterogeneity. Results Fourteen articles including 24 independent studies (16 compared LAMP to CRS, 8 to culture) of EPTB were identified. LAMP showed a pooled sensitivity of 77% (95% confidence interval (CI) 68–85), specificity of 99% (95% CI 96–100), and area under SROC curves (AUC) of 0.96 (95% CI 0.94–0.97) against CRS. It showed a pooled sensitivity of 93% (95% CI 88–96), specificity of 77% (95% CI 64–86), and AUC of 0.94 (95% CI 0.92–0.96) against culture. The pooled sensitivity, specificity, and AUC of MPB64 LAMP were 86% (95% CI 86–86), 100% (95% CI 100–100), and 0.97 (95% CI 0.95–0.98), respectively, and those of IS6110 LAMP were 75% (95% CI 64–84), 99% (95% CI 90–100), and 0.91 (95% CI 0.88–0.93), respectively, compared with CRS. Conclusions These results suggest good diagnostic efficacy of LAMP in the detection of EPTB. Additionally, the diagnostic efficacy of MPB64 LAMP was superior to that of IS6110 LAMP.
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Affiliation(s)
- Guocan Yu
- Department of Thoracic Surgery, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Yanqin Shen
- Department of Tuberculosis, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Fangming Zhong
- Department of Thoracic Surgery, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Bo Ye
- Department of Thoracic Surgery, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Jun Yang
- Department of Thoracic Surgery, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
| | - Gang Chen
- Department of Thoracic Surgery, Hangzhou Red Cross Hospital, Hangzhou, Zhejiang, China
- * E-mail:
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Fan L, Li D, Zhang S, Yao L, Hao X, Gu J, Li H, Niu J, Zhang Z, Zhu C. Parallel Tests Using Culture, Xpert MTB/RIF, and SAT-TB in Sputum Plus Bronchial Alveolar Lavage Fluid Significantly Increase Diagnostic Performance of Smear-Negative Pulmonary Tuberculosis. Front Microbiol 2018; 9:1107. [PMID: 29973917 PMCID: PMC6020777 DOI: 10.3389/fmicb.2018.01107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/08/2018] [Indexed: 11/18/2022] Open
Abstract
At present, tuberculosis remains a serious threat to human health. The diagnosis of pulmonary tuberculosis (PTB) is still difficult, and the prominent challenge for diagnosis is the lack of a highly sensitive and specific method. In order to explore the diagnostic value of parallel tests, this study prospectively enrolled 258 patients with smear-negative PTB from May 2, 2015 to December 31, 2016. The sputum specimens and bronchial alveolar lavage fluid (BALF) samples from all patients were assessed for MTB detection by culture, Xpert MTB/RIF, and simultaneous amplification and testing method for TB (SAT-TB). Overall, the sensitivity of any single test using culture, Xpert MTB/RIF, or SAT-TB was lower than that for parallel tests (p < 0.05), and the sensitivity rates for MTB detection in BALF were significantly higher than those in sputum samples. There were lower agreements in the detection results between sputum samples and BALF for all tests (p < 0.05). The parallel tests models of using culture plus Xpert MTB/RIF plus SAT-TB, culture plus Xpert, or culture plus SAT-TB achieved higher sensitivities compared with all three single test models (p < 0.05). Additionally, joint detection using sputum and BALF samples achieved a high sensitivity (0.8566, 95% CI: 0.8086–0.8941). In conclusion, the parallel tests model using culture, Xpert MTB/RIF, and SAT-TB in sputum plus BALF significantly increases the diagnostic performance of smear-negative PTB; thus, this method should be applied clinically when PTB is suspected but smear results are negative.
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Affiliation(s)
- Lin Fan
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Danfeng Li
- Department of Laboratory Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shaojun Zhang
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lan Yao
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaohui Hao
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jin Gu
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hong Li
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinxia Niu
- Department of Laboratory Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zhemin Zhang
- Clinic and Research Center of Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Changtai Zhu
- Department of Laboratory Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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Seki M, Kim CK, Hayakawa S, Mitarai S. Recent advances in tuberculosis diagnostics in resource-limited settings. Eur J Clin Microbiol Infect Dis 2018; 37:1405-1410. [DOI: 10.1007/s10096-018-3258-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
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