1
|
Patnaik N, Dey RJ. Label-Free Citrate-Stabilized Silver Nanoparticles-Based, Highly Sensitive, Cost-Effective, and Rapid Visual Method for the Differential Detection of Mycobacterium tuberculosis and Mycobacterium bovis. ACS Infect Dis 2024; 10:426-435. [PMID: 38112513 DOI: 10.1021/acsinfecdis.3c00390] [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: 12/21/2023]
Abstract
Tuberculosis poses a global health challenge, and it demands improved diagnostics and therapies. Distinguishing between Mycobacterium tuberculosis (M. tb) and Mycobacterium bovis (M. bovis) infections holds critical "One Health" significance due to the zoonotic nature of these infections and inherent resistance of M. bovis to pyrazinamide, a key part of the directly observed treatment, short-course (DOTS) regimen. Furthermore, most of the currently used molecular detection methods fail to distinguish between the two species. To address this, our study presents an innovative molecular-biosensing strategy. We developed a label-free citrate-stabilized silver nanoparticle aggregation assay that offers sensitive, cost-effective, and swift detection. For molecular detection, genomic markers unique to M. tb and M. bovis were targeted using species-specific primers. In addition to amplifying species-specific regions, these primers also aid the detection of characteristic deletions in each of the mycobacterial species. Post polymerase chain reaction (PCR), we compared two highly sensitive visual detection methods with respect to the traditional agarose gel electrophoresis. The paramagnetic bead-based bridging flocculation assay successfully discriminates M. tb from M. bovis with a sensitivity of ∼40 bacilli. The second strategy exploits citrate-stabilized silver nanoparticles, which aggregate in the absence of amplified dsDNA on the addition of sodium chloride (NaCl). This technique enables the precise, sensitive, and differential detection of as few as ∼4 bacilli. Our study hence advances tuberculosis detection, overcoming the challenges of M. tb and M. bovis differentiation and offering a quicker alternative to time-consuming methods.
Collapse
Affiliation(s)
- Naresh Patnaik
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad, Telangana State 500078, India
| | - Ruchi Jain Dey
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad, Telangana State 500078, India
| |
Collapse
|
2
|
Nan X, Yao X, Yang L, Cui Y. Lateral flow assay of pathogenic viruses and bacteria in healthcare. Analyst 2023; 148:4573-4590. [PMID: 37655501 DOI: 10.1039/d3an00719g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Healthcare-associated pathogenic viruses and bacteria can have a serious impact on human health and have attracted widespread global attention. The lateral flow assay is a unidirectional detection based on the binding of a target analyte and a bioreceptor on the device via lateral flow. With incredible advantages over traditional chromatographic methods, such as rapid detection, ease of manufacture and cost effectiveness, these test strips are increasingly considered the ideal form for point-of-care applications. This review explores lateral flow assays for pathogenic viruses and bacteria, with a particular focus on methodologies, device components, construction methods, and applications. We anticipate that this review could provide exciting opportunities for developing new lateral flow devices for pathogens and advance related healthcare applications.
Collapse
Affiliation(s)
- Xuanxu Nan
- School of Materials Science and Engineering, Peking University; First Hospital Interdisciplinary Research Center, Peking University, Beijing 100871, P.R. China.
| | - Xuesong Yao
- School of Materials Science and Engineering, Peking University; First Hospital Interdisciplinary Research Center, Peking University, Beijing 100871, P.R. China.
| | - Li Yang
- Peking University First Hospital; Peking University Institute of Nephrology, Beijing 100034, P. R. China.
| | - Yue Cui
- School of Materials Science and Engineering, Peking University; First Hospital Interdisciplinary Research Center, Peking University, Beijing 100871, P.R. China.
| |
Collapse
|
3
|
Mukherjee S, Perveen S, Negi A, Sharma R. Evolution of tuberculosis diagnostics: From molecular strategies to nanodiagnostics. Tuberculosis (Edinb) 2023; 140:102340. [PMID: 37031646 PMCID: PMC10072981 DOI: 10.1016/j.tube.2023.102340] [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: 01/19/2023] [Revised: 03/12/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
Tuberculosis has remained a global concern for public health affecting the lives of people for ages. Approximately 10 million people are affected by the disease and 1.5 million succumb to the disease worldwide annually. The COVID-19 pandemic has highlighted the role of early diagnosis to win the battle against such infectious diseases. Thus, advancement in the diagnostic approaches to provide early detection forms the foundation to eradicate and manage contagious diseases like tuberculosis. The conventional diagnostic strategies include microscopic examination, chest X-ray and tuberculin skin test. The limitations associated with sensitivity and specificity of these tests demands for exploring new techniques like probe-based assays, CRISPR-Cas and microRNA detection. The aim of the current review is to envisage the correlation between both the conventional and the newer approaches to enhance the specificity and sensitivity. A significant emphasis has been placed upon nanodiagnostic approaches manipulating quantum dots, magnetic nanoparticles, and biosensors for accurate diagnosis of latent, active and drug-resistant TB. Additionally, we would like to ponder upon a reliable method that is cost-effective, reproducible, require minimal infrastructure and provide point-of-care to the patients.
Collapse
Affiliation(s)
| | - Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anjali Negi
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
4
|
A Comparative Study on Visual Detection of Mycobacterium tuberculosis by Closed Tube Loop-Mediated Isothermal Amplification: Shedding Light on the Use of Eriochrome Black T. Diagnostics (Basel) 2023; 13:diagnostics13010155. [PMID: 36611447 PMCID: PMC9818645 DOI: 10.3390/diagnostics13010155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/29/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Loop-mediated isothermal amplification is a promising candidate for the rapid detection of Mycobacterium tuberculosis. However, the high potential for carry-over contamination is the main obstacle to its routine use. Here, a closed tube LAMP was intended for the visual detection of Mtb to compare turbidimetric and two more favorable colorimetric methods using calcein and hydroxy naphthol blue (HNB). Additionally, a less studied dye (i.e., eriochrome black T (EBT)) was optimized in detail in the reaction for the first time. Mtb purified DNA and 30 clinical specimens were used to respectively determine the analytical and diagnostic sensitivities of each method. The turbidimetric method resulted in the best analytical sensitivity (100 fg DNA/reaction), diagnostic sensitivity and specificity (100%), and time-to-positivity of the test (15 min). However, this method is highly prone to subjective error in reading the results. Moreover, HNB-, calcein-, and EBT-LAMP could respectively detect 100 fg, 1 pg, and 1 pg DNA/reaction (the analytical sensitivities) in 30, 15, and 30 min, while the diagnostic sensitivity and specificity were respectively 93.3% and 100% for them all. Interestingly, EBT-LAMP showed the lowest potential for subjective error in reading the results. This report helps judiciously choose the most appropriate visual method, taking a step forward toward the field applicability of LAMP for the detection of Mtb, particularly in resource-limited settings.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
WITHDRAWN: Analysis of the application value of molecular diagnostic technology of mycobacterium tuberculosis. J Clin Tuberc Other Mycobact Dis 2022. [DOI: 10.1016/j.jctube.2022.100330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
7
|
Erber AC, Sandler PJ, de Avelar DM, Swoboda I, Cota G, Walochnik J. Diagnosis of visceral and cutaneous leishmaniasis using loop-mediated isothermal amplification (LAMP) protocols: a systematic review and meta-analysis. Parasit Vectors 2022; 15:34. [PMID: 35073980 PMCID: PMC8785018 DOI: 10.1186/s13071-021-05133-2] [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: 08/24/2020] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Sensitive, reliable and fast diagnostic tools that are applicable in low-resource settings, at the point of care (PoC), are seen as crucial in the fight against visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). Addressing the need for a PoC test, several diagnostic tests, including serological and molecular methods, have been developed and evaluated in the past. One promising molecular method, already implemented for diagnosis of a range of diseases, is the loop-mediated isothermal amplification (LAMP) protocol. In this systematic review and meta-analysis, using a comprehensive search strategy, we focus on studies evaluating the performance of LAMP for the diagnosis of leishmaniasis in humans and other mammals such as dogs, compared with microscopy and/or any other molecular diagnostic method. A meta-analysis, pooling sensitivity and specificity rates and calculating areas under the curve (AUCs) in summary receiver operating characteristic (SROC) plots, was conducted on datasets extracted from studies, grouped by clinical condition and sample type. We found high sensitivity and specificity for LAMP when compared with microscopy and PCR using blood samples, with pooled estimate values of > 90% for all subgroups, corresponding to calculated AUC values > 0.96, except for LAMP compared to microscopy for diagnosis of CL. However, only a limited number of studies were truly comparable. Most of the observed heterogeneity is likely based on true differences between the studies rather than sampling error only. Due to simple readout methods and low laboratory equipment requirements for sample preparation compared to other molecular methods, LAMP is a promising candidate for a molecular (near-)PoC diagnostic method for VL and CL.
Collapse
Affiliation(s)
- Astrid Christine Erber
- Department of Epidemiology, Center for Public Health, Medical University of Vienna, Kinderspitalgasse 15, 1st floor, 1090, Vienna, Austria. .,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, New Richards Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LG, UK.
| | - Peter Julian Sandler
- Department of Applied Life Sciences, FH Campus Wien University of Applied Sciences, Helmut-Qualtinger Gasse 2, 1030, Vienna, Austria
| | - Daniel Moreira de Avelar
- Pesquisa Clínica e Políticas Públicas em Doenças Infecciosas e Parasitárias, Instituto René Rachou-Fundação Oswaldo Cruz, Fiocruz, Belo Horizonte, Minas Gerais, Brazil
| | - Ines Swoboda
- Department of Applied Life Sciences, FH Campus Wien University of Applied Sciences, Helmut-Qualtinger Gasse 2, 1030, Vienna, Austria
| | - Gláucia Cota
- Pesquisa Clínica e Políticas Públicas em Doenças Infecciosas e Parasitárias, Instituto René Rachou-Fundação Oswaldo Cruz, Fiocruz, Belo Horizonte, Minas Gerais, Brazil
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Homayoonnia S, Lee Y, Andalib D, Rahman MS, Shin J, Kim K, Kim S. Micro/nanotechnology-inspired rapid diagnosis of respiratory infectious diseases. Biomed Eng Lett 2021; 11:335-365. [PMID: 34513114 PMCID: PMC8424173 DOI: 10.1007/s13534-021-00206-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/17/2021] [Accepted: 08/29/2021] [Indexed: 12/18/2022] Open
Abstract
Humans have suffered from a variety of infectious diseases since a long time ago, and now a new infectious disease called COVID-19 is prevalent worldwide. The ongoing COVID-19 pandemic has led to research of the effective methods of diagnosing respiratory infectious diseases, which are important to reduce infection rate and help the spread of diseases be controlled. The onset of COVID-19 has led to the further development of existing diagnostic methods such as polymerase chain reaction, reverse transcription polymerase chain reaction, and loop-mediated isothermal amplification. Furthermore, this has contributed to the further development of micro/nanotechnology-based diagnostic methods, which have advantages of high-throughput testing, effectiveness in terms of cost and space, and portability compared to conventional diagnosis methods. Micro/nanotechnology-based diagnostic methods can be largely classified into (1) nanomaterials-based, (2) micromaterials-based, and (3) micro/nanodevice-based. This review paper describes how micro/nanotechnologies have been exploited to diagnose respiratory infectious diseases in each section. The research and development of micro/nanotechnology-based diagnostics should be further explored and advanced as new infectious diseases continue to emerge. Only a handful of micro/nanotechnology-based diagnostic methods has been commercialized so far and there still are opportunities to explore.
Collapse
Affiliation(s)
- Setareh Homayoonnia
- Department of Mechanical and Manufacturing Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Yoonjung Lee
- Department of Mechanical and Manufacturing Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Daniyal Andalib
- Department of Mechanical and Manufacturing Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Md Sazzadur Rahman
- Department of Mechanical and Manufacturing Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Jaemyung Shin
- Biomedical Engineering Graduate Program, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Keekyoung Kim
- Department of Mechanical and Manufacturing Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4 Canada
- Biomedical Engineering Graduate Program, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Seonghwan Kim
- Department of Mechanical and Manufacturing Engineering, Schulich School of Engineering, University of Calgary, Calgary, AB T2N 1N4 Canada
| |
Collapse
|
10
|
Zhang Z, Du J, Liu T, Wang F, Jia J, Dong L, Zhao L, Xue Y, Jiang G, Yu X, Huang H. EasyNAT MTC assay: A simple, rapid, and low-cost cross-priming amplification method for the detection of mycobacterium tuberculosis suitable for point-of-care testing. Emerg Microbes Infect 2021; 10:1530-1535. [PMID: 34288833 PMCID: PMC8330774 DOI: 10.1080/22221751.2021.1959271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
More sensitive, rapid, and affordable diagnostic tools for pulmonary tuberculosis (PTB) are urgently needed. This study aimed to assess the performance of EasyNAT MTC (abbreviation: EasyNAT) (Ustar Biotechnologies, China), a novel isothermal amplification method with a turnaround time of less than two hours that requires a few manual steps to process the sputum. Sputum samples from 249 patients with suspected PTB were subjected to smear, culture, Xpert MTB/RIF (Cepheid, USA) and EasyNAT assay testing. Of the 169 PTB patients, EasyNAT detected more PTB patients than Xpert (72.19% vs. 61.54%, P < 0.05, χ2 = 4.326). Both the Xpert assay and EasyNAT assay detected almost all the culture-positive sputa successfully, but EasyNAT yielded more positive results among the smear-negative and culture-negative PTB cases (44.59% (33/74) vs. 22.97% (17/74), P < 0.01, χ2 = 7.732). Although the specificity of EasyNAT was lower in contrast to Xpert [95.00% (76/80) vs. 98.75% (79/80)], the difference was not significant (P = 0.363, χ2 = 0.826). EasyNAT could be used as an initial test for PTB diagnosis due to its simplicity, rapid turnaround time, high sensitivity, and low cost.
Collapse
Affiliation(s)
- Zhuman Zhang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Jian Du
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Tao Liu
- Department of Anesthesiology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Fen Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Junnan Jia
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Lingling Dong
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Liping Zhao
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Yi Xue
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, People's Republic of China
| |
Collapse
|
11
|
Akapelwa ML, Kapalamula TF, Ouchi-Aizu Y, Hang'ombe BM, Nishiuchi Y, Gordon SV, Solo ES, Tamaru A, Nishimura T, Hasegawa N, Morimoto K, Fukushima Y, Suzuki Y, Nakajima C. Evaluation of IS1245 LAMP in Mycobacterium avium and the influence of host-related genetic diversity on its application. Diagn Microbiol Infect Dis 2021; 101:115494. [PMID: 34391980 DOI: 10.1016/j.diagmicrobio.2021.115494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
Early detection and treatment are paramount for the timely control of Mycobacterium avium infections. Herein, we designed a LAMP assay targeting a widely used species-specific marker IS1245 for the rapid detection of M. avium and evaluated its applicability using human (n = 137) and pig (n = 91) M. avium isolates from Japan. The developed assay could detect as low as 1 genome copy of M. avium DNA within 30 minutes. All 91 (100%) M. avium isolates from pigs were detected positive while all other tested bacterial species were negative. Interestingly, among the 137 clinical M. avium isolates, 41 (30%) were undetectable with this LAMP assay as they lacked IS1245, the absence of which was revealed by PCR and whole-genome sequencing. These findings highlighted genotypic differences in M. avium strains from humans and pigs in Japan and how this diversity can influence the applicability of a detection tool across different geographic areas and hosts.
Collapse
Affiliation(s)
- Mwangala Lonah Akapelwa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Thoko Flav Kapalamula
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Yuki Ouchi-Aizu
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Bernard Mudenda Hang'ombe
- Department of ParaClinicals, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia; Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Eddie Samuneti Solo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Aki Tamaru
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | | | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Kozo Morimoto
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan.
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan.
| |
Collapse
|
12
|
Ablordey A, Ahotor E, Narh CA, King SA, Cruz I, Ndung'u JM, de Souza DK. Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens. BMC Infect Dis 2021; 21:598. [PMID: 34162342 PMCID: PMC8220662 DOI: 10.1186/s12879-021-06308-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/10/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Early diagnosis and treatment of Buruli ulcer is critical in order to avoid the debilitating effects of the disease. In this regard, the development of new diagnostic and point of care tools is encouraged. The loop-mediated isothermal amplification for the detection of Mycobacterium ulcerans represents one of the new tools with a good potential of being developed into a point of care test. There is however the need to standardize the assays, reduce sample preparation times, improve the detection/visualization system and optimize them for high-throughput screening, adaptable to low resourced laboratories. METHODS In this study, we assessed two DNA extraction protocols (modified Boom and EasyNAT methods), three previously published LAMP primer sets (BURULI, MU 2404 and BU-LAMP), and compared the sensitivity and specificity of LAMP assays on three DNA amplification platforms. RESULTS Our results show that Buruli ulcer diagnosis using primers targeting IS2404 for the LAMP method is sensitive (73.75-91.49%), depending on the DNA extraction method used. Even though the modified Boom DNA extraction method provided the best results, its instrumentation requirement prevent it from being field applicable. The EasyNAT method on the other hand is simpler and may represent the best method for DNA extraction in less resourced settings. CONCLUSIONS For further work on the development and use of LAMP tests for Buruli diagnosis, it is recommended that the BURULI sets of primers be used, as these yielded the best results in terms of sensitivity (87.50-91.49%) and specificity (89.23-100%), depending on the DNA extraction methods used.
Collapse
Affiliation(s)
- Anthony Ablordey
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana.
| | - Evans Ahotor
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Charles A Narh
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Sandra A King
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Isra Cruz
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
- National School of Public Health, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Dziedzom K de Souza
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| |
Collapse
|
13
|
Wang X, Wang G, Wang Y, Quan S, Qi H, Sun L, Shen C, Huang H, Jiao W, Shen A. Development and Preliminary Application of Multiplex Loop-Mediated Isothermal Amplification Coupled With Lateral Flow Biosensor for Detection of Mycobacterium tuberculosis Complex. Front Cell Infect Microbiol 2021; 11:666492. [PMID: 33987108 PMCID: PMC8110928 DOI: 10.3389/fcimb.2021.666492] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/07/2021] [Indexed: 12/27/2022] Open
Abstract
The aim of this study was to develop a simple and reliable method to detect Mycobacterium tuberculosis complex (MTBC) and verify its clinical application preliminarily. A loop-mediated isothermal amplification method coupled with lateral flow biosensor (LAMP-LFB) assay, was developed and evaluated for detection of MTBC. Two sets of primers, which targeted IS6110 and IS1081 sequences of MTBC, were designed for establishment of multiplex LAMP-LFB assay. The amplicons were labelled with biotin and fluorescein isothiocyanate (FITC) by adding FITC labelled primer and biotin-14-dATP and biotin-14-dCTP and could be visualized using LFB. The optimal reaction conditions of multiplex LAMP-LFB assay confirmed were 66°C for 50 min. The analytical sensitivity of multiplex LAMP-LFB is 10 fg of genomic templates using pure culture, and no cross-reactivity with other common bacteria and non-tuberculous mycobacteria strains was obtained. A total of 143 clinical samples collected from 100 TB patients (62 definite TB cases and 38 probable TB cases) and 43 non-TB patients were used for evaluating the feasibility of multiplex LAMP-LFB assay. The multiplex LAMP-LFB (82.0%, 82/100) showed higher sensitivity than culture (47.0%, 47/100, P < 0.001) and Xpert MTB/RIF (54.0%, 54/100, P < 0.001). Importantly, the multiplex LAMP-LFB assay detected additional 28 probable TB cases, which increased the percentage of definite TB cases from 62.0% (62/100) to 90.0% (90/100). The specificity of multiplex LAMP-LFB assay in patients without TB was 97.7% (42/43). Therefore, multiplex LAMP-LFB assay is a simple, reliable, and sensitive method for MTBC detection, especially in probable TB cases and resource limited settings.
Collapse
Affiliation(s)
- Xingyun Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Guirong Wang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yacui Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Shuting Quan
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hui Qi
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Chen Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hairong Huang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Weiwei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Adong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
14
|
Kapalamula TF, Thapa J, Akapelwa ML, Hayashida K, Gordon SV, Hang' ombe BM, Munyeme M, Solo ES, Bwalya P, Nyenje ME, Tamaru A, Suzuki Y, Nakajima C. Development of a loop-mediated isothermal amplification (LAMP) method for specific detection of Mycobacterium bovis. PLoS Negl Trop Dis 2021; 15:e0008996. [PMID: 33493196 PMCID: PMC7833227 DOI: 10.1371/journal.pntd.0008996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/14/2020] [Indexed: 11/24/2022] Open
Abstract
Bovine tuberculosis (TB) caused by Mycobacterium bovis is a significant health threat to cattle and a zoonotic threat for humans in many developing countries. Rapid and accurate detection of M. bovis is fundamental for controlling the disease in animals and humans, and for the proper treatment of patients as one of the first-line anti-TB drug, pyrazinamide, is ineffective against M. bovis. Currently, there are no rapid, simplified and low-cost diagnostic methods that can be easily integrated for use in many developing countries. Here, we report the development of a loop-mediated isothermal amplification (LAMP) assay for specific identification of M. bovis by targeting the region of difference 4 (RD4), a 12.7 kb genomic region that is deleted solely in M. bovis. The assay's specificity was evaluated using 139 isolates comprising 65 M. bovis isolates, 40 M. tuberculosis isolates, seven M. tuberculosis complex reference strains, 22 non-tuberculous mycobacteria and five other bacteria. The established LAMP detected only M. bovis isolates as positive and no false positives were observed using the other mycobacteria and non-mycobacteria tested. Our LAMP assay detected as low as 10 copies of M. bovis genomic DNA within 40 minutes. The procedure of LAMP is simple with an incubation at a constant temperature. Results are observed with the naked eye by a color change, and there is no need for expensive equipment. The established LAMP can be used for the detection of M. bovis infections in cattle and humans in resource-limited areas. Although bovine tuberculosis in humans has been eliminated in developed countries, the disease remains a challenge in many developing countries. Routine laboratory methods used to identify tuberculosis (TB) in high-burden countries do not distinguish between the two main causes of TB in humans, namely Mycobacterium tuberculosis and M. bovis. In addition, M. bovis is naturally resistant to one of the first-line drugs used to treat TB called pyrazinamide; therefore, accurate diagnosis of M. bovis is important for proper selection of anti TB drugs. In cattle, surveillance for M. bovis infection is important to obtain data on bovine TB burden and hence provide a basis for the establishment and/or improvement of control programs. In this study, a loop-mediated isothermal amplification (LAMP) based method was developed to identify M. bovis. This LAMP method detected M. bovis within 40 minutes following incubation at constant temperature (66°C) in a battery-powered incubator and results could be read with the naked eye following development of a color change. Our results elaborate a rapid and low-cost LAMP based method for detection and surveillance of M. bovis infection in cattle and humans in resource-limited, endemic areas.
Collapse
Affiliation(s)
- Thoko Flav Kapalamula
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Jeewan Thapa
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mwangala Lonah Akapelwa
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kyoko Hayashida
- Division of Collaborations and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Contsrol, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Stephen V. Gordon
- International Collaboration Unit, Research Center for Zoonosis Contsrol, Hokkaido University, Sapporo, Hokkaido, Japan
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Bernard Mudenda Hang' ombe
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Musso Munyeme
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Eddie Samuneti Solo
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Precious Bwalya
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Department of Pathology and Microbiology, University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Mirriam Ethel Nyenje
- Community Health Sciences Unit, National Tuberculosis Reference Laboratory, Lilongwe, Malawi
| | - Aki Tamaru
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Contsrol, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Contsrol, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail:
| |
Collapse
|
15
|
Patra S, Kalwaje Eshwara V, Pai AR, Varma M, Mukhopadhyay C. Evaluation of clinical, diagnostic features and therapeutic outcome of neurobrucellosis: a case series and review of literature. Int J Neurosci 2021; 132:1080-1090. [PMID: 33287603 DOI: 10.1080/00207454.2020.1860969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AIM In this study, we aimed to discuss the clinical features, laboratory findings, treatment and outcome of seven cases of neurobrucellosis from a tertiary care center and review the available global literature. MATERIALS AND METHODS The diagnosis of neurobrucellosis was established using the following criteria in our setting: (1) signs and symptoms of neurological infection with examination of cerebrospinal fluid (CSF) revealing signs of meningitis, (2) isolation of Brucella spp. from blood and/or CSF and/or antibody titer ≥1:160 in serum using standard agglutination test (SAT) and/or the presence of anti-Brucella antibodies in CSF and/or detection of Brucella spp.-specific DNA from CSF using PCR. A literature search was performed to review previous cases of neurobrucellosis published worldwide during the last 30 years. RESULTS The proportion of neurobrucellosis was 2.8% in our setting. Fever with headache and altered sensorium were the major presenting complaints. Brucella melitensis was isolated from blood culture in 6 patients. From the literature search, a total of 221 cases of neurobrucellosis were reviewed and analyzed. Meningitis (32.6%), loss of hearing (25.8%) and encephalitis (14.9%) were the most common clinical features. Involvement of cranial nerves, polyradiculopathy and paraplegia were the major complications found in patients with neurobrucellosis. CONCLUSIONS Neurobrucellosis should always be considered in the differential diagnosis of befitting neurological, rheumatological, and neuropsychiatric presentations in endemic regions for brucellosis. To prevent morbidity and mortality associated with neurobrucellosis, a multimodal diagnostic approach is essential for early and accurate diagnosis and effective treatment.
Collapse
Affiliation(s)
- Sudipta Patra
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vandana Kalwaje Eshwara
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Aparna Ramakrishna Pai
- Department of Neurology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Muralidhar Varma
- Department of Infectious Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chiranjay Mukhopadhyay
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India.,Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| |
Collapse
|
16
|
Sreedeep K, Sethi S, Yadav R, Vaidya PC, Angurana SK, Saini A, Mehra N, Singh M. Loop-mediated isothermal amplification (LAMP) in the respiratory specimens for the diagnosis of pediatric pulmonary tuberculosis: A pilot study. J Infect Chemother 2020; 26:823-830. [DOI: 10.1016/j.jiac.2020.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 11/28/2022]
|
17
|
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.
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Acharya B, Acharya A, Gautam S, Ghimire SP, Mishra G, Parajuli N, Sapkota B. Advances in diagnosis of Tuberculosis: an update into molecular diagnosis of Mycobacterium tuberculosis. Mol Biol Rep 2020; 47:4065-4075. [DOI: 10.1007/s11033-020-05413-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/28/2020] [Indexed: 01/02/2023]
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Advances in Directly Amplifying Nucleic Acids from Complex Samples. BIOSENSORS-BASEL 2019; 9:bios9040117. [PMID: 31574959 PMCID: PMC6955841 DOI: 10.3390/bios9040117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.
Collapse
|
22
|
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: 18] [Impact Index Per Article: 3.6] [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.
Collapse
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.
| |
Collapse
|
23
|
Sharma G, Tewari R, Dhatwalia SK, Yadav R, Behera D, Sethi S. A loop-mediated isothermal amplification assay for the diagnosis of pulmonary tuberculosis. Lett Appl Microbiol 2019; 68:219-225. [PMID: 30636048 DOI: 10.1111/lam.13115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/08/2018] [Accepted: 10/08/2018] [Indexed: 11/28/2022]
Abstract
Quantitated Mycobacterium tuberculosis (M.tb) H37Rv DNA was used to analyse the sensitivity and the specificity was assessed using DNA isolated from the reference strain H37Rv, 12 nontuberculous mycobacterium (NTM) species and five nonmycobacterium species. Furthermore, performance of the assay was evaluated on the sputum samples and compared with smear microscopy, culture and PCR. mpt64 (also called mpb64 or Rv1980c) loop-mediated isothermal amplification (LAMP) successfully detected 1 pg DNA within 40 min and successfully rejected NTMs and other bacterial species tested. It specifically detected all the 119 confirmed TB cases and 100 of the 104 control cases. The resulting sensitivity and specificity of LAMP assay was found to be 100% (95% CI: 96·79-100%) and 96·15% (95% CI; 90·44-98·94%) respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Loop-mediated isothermal amplification (LAMP) is a technique for isothermal DNA amplification suitable for cost-limited settings as it prevents the use of sophisticated instruments. Using mpt64 antigenic protein gene, we developed a LAMP assay especially for organisms of the M. tuberculosis complex. mpt64 LAMP assay showed 100% sensitivity and detected all the bacteriologically and clinically positive TB cases not detected by smear, culture or PCR methods.
Collapse
Affiliation(s)
- G Sharma
- Department of Microbial Biotechnology, Panjab University, Chandigarh, India
| | - R Tewari
- Department of Microbial Biotechnology, Panjab University, Chandigarh, India
| | - S K Dhatwalia
- Department of Biophysics, Panjab University, Chandigarh, India
| | - R Yadav
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - D Behera
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - S Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
24
|
Niu L, Zhao F, Chen J, Nong J, Wang C, Wang J, Gao N, Zhu X, Wu L, Hu S. Isothermal amplification and rapid detection of Klebsiella pneumoniae based on the multiple cross displacement amplification (MCDA) and gold nanoparticle lateral flow biosensor (LFB). PLoS One 2018; 13:e0204332. [PMID: 30273362 PMCID: PMC6166938 DOI: 10.1371/journal.pone.0204332] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/06/2018] [Indexed: 11/18/2022] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a frequent pathogen causing nosocomial infections and outbreaks. We developed a multiple cross displacement amplification (MCDA) assay for the detection of K. pneumoniae, which can get the positive results within 40 minutes’ isothermal amplification. Gold-nanoparticle lateral flow biosensor (LFB) and colorimetric indicators were used for the rapid readouts of MCDA amplification. The detection limit of this assay was 100 fg per reaction at 65°C, which was confirmed to be the optimal amplification temperature according to the real time turbidimeters. For specificity, all of the 30 clinical-source K. pneumoniae strains were positive for the MCDA, and all of the non-K. pneumoniae strains belonging to 31 different species were negative for this MCDA assay. To evaluate the practical applicability of this method, we assessed its detection limit for K. pneumoniae strains in sputum samples (24 CFU per reaction), and DNA templates of 100 sputum samples further underwent the MCDA-LFB tests. All of the sputum samples being positive for K. pneumoniae (30/100) with the culture method were successfully identified with the MCDA assay, the detection power of which was higher than that of polymerase chain reaction (PCR) (25/100). Thus, the MCDA test for K. pneumoniae combined with the gold nanoparticle LFB as the results readout scheme, are simple, specific, and sensitive methods for the rapid diagnosis of K. pneumoniae in clinical samples.
Collapse
Affiliation(s)
- Lina Niu
- Department of Pathogen Biology, School of Basic Medicine and Lifescience, Hainan Medical University, Haikou, Hainan, China
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Fan Zhao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Jinlong Chen
- Department of Pathogen Biology, School of Basic Medicine and Lifescience, Hainan Medical University, Haikou, Hainan, China
| | - Jinqing Nong
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Chunmei Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Jing Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Naishu Gao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Xiaoxue Zhu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Lei Wu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Shoukui Hu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
- * E-mail:
| |
Collapse
|
25
|
Eddabra R, Ait Benhassou H. Rapid molecular assays for detection of tuberculosis. Pneumonia (Nathan) 2018; 10:4. [PMID: 29876241 PMCID: PMC5968606 DOI: 10.1186/s41479-018-0049-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease that remains an important public health problem at the global level. It is one of the main causes of morbidity and mortality, due to the emergence of antibiotic resistant Mycobacterium strains and HIV co-infection. Over the past decade, important progress has been made for better control of the disease. While microscopy and culture continue to be indispensible for laboratory diagnosis of tuberculosis, the range of several molecular diagnostic tests, including the nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have expanded tremendously. They are becoming more accessible not only for detection and identification of Mycobacterium tuberculosis complex in clinical specimens, but now extend to diagnosing multi-drug resistant strains. Molecular diagnostic tests provide timely results useful for high-quality patient care, low contamination risk, and ease of performance and speed. This review focuses on the current diagnostic tests in use, including emerging technologies used for detection of tuberculosis in clinical specimens. The sensitivity and specificity of these tests have also been taken into consideration.
Collapse
Affiliation(s)
- Rkia Eddabra
- Higher Institute of Nursing Professions and Health Techniques, Avenue Colonnel Major Habbouha Oueld Laâbid. Madinat Al Wahda I, Laayoune, Morocco
| | - Hassan Ait Benhassou
- Medical Biotechnology Center, Moroccan Foundation for Advanced Science, Innovation and Research (MAScIR), Rabat Design Center, Avenue Mohamed El Jazouli - Madinat Al Irfane, 10100 Rabat, Morocco
| |
Collapse
|
26
|
Kaewphinit T, Ckumdee J, Chansiri K, Santiwatanakul S. Development and evaluation of a loop-mediated isothermal amplification combined with au-nanoprobe assay for rapid detection of Mycobacterium tuberculosis. Indian J Med Microbiol 2018; 35:302-304. [PMID: 28681828 DOI: 10.4103/ijmm.ijmm_15_333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has been proposed as an inexpensive and easy to perform assay for molecular diagnostics. We present a novel strategy for the detection of LAMP amplicons derived from Mycobacterium tuberculosis by the use of Au-nanoprobes. When applied to a total of 93 clinical specimens, the LAMP assay demonstrated sensitivity and specificity higher than that of polymerase chain reaction and culture. The Au-nanoprobe augmented LAMP test platform with its advantages of robust reagents and a simple colorimetric detection method can be adapted easily for the rapid detection of other infectious disease agents at a low cost.
Collapse
Affiliation(s)
- Thongchai Kaewphinit
- Innovative Learning Center, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Jutturong Ckumdee
- Department of Clinical Pathology, Faculty of Medicine, Vajira Hospital, Navamindradhiraj University, Bangkok 10110, Thailand
| | - Kosum Chansiri
- Department of Biochemistry, Faculty of Medicine, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Somchai Santiwatanakul
- Department of Pathology, Faculty of Medicine, Srinakharinwirot University, Bangkok 10110, Thailand
| |
Collapse
|
27
|
Shchit IY, Ignatov KB, Kudryavtseva TY, Shishkova NA, Mironova RI, Marinin LI, Mokrievich AN, Kramarov VM, Biketov SF, Dyatlov IA. The use of loop-mediated isothermal DNA amplification for the detection and identification of the anthrax pathogen. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2017; 32:100-108. [PMID: 32214650 PMCID: PMC7088587 DOI: 10.3103/s0891416817020094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Indexed: 01/16/2023]
Abstract
The results of detection and identification of Bacillus anthracis strains in loop-mediated isothermal DNA amplification (LAMP) reaction performed under optimized conditions with original primers and thermostable DNA polymerase are presented. Reproducible LAMP-based detection of chromosomal and plasmid DNA targets specific for B. anthracis strains has been demonstrated. No cross reactions with DNA from bacterial strains of other species of the B. cereus group were detected. The development of tests for anthrax-pathogen detection based on the optimized reaction of loop isothermal DNA amplification is planned. These tests will be convenient for clinical studies and field diagnostics due to the absence of requirements for sophisticated equipment.
Collapse
Affiliation(s)
- I Yu Shchit
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - K B Ignatov
- 2Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 117971 Russia.,3All-Russian Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127422 Russia
| | - T Yu Kudryavtseva
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - N A Shishkova
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - R I Mironova
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - L I Marinin
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - A N Mokrievich
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - V M Kramarov
- 2Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 117971 Russia.,3All-Russian Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127422 Russia
| | - S F Biketov
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - I A Dyatlov
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| |
Collapse
|
28
|
Sethi S, Dhaliwal L, Dey P, Kaur H, Yadav R, Sethi S. Loop-mediated isothermal amplification assay for detection of Mycobacterium tuberculosis complex in infertile women. Indian J Med Microbiol 2017; 34:322-7. [PMID: 27514954 DOI: 10.4103/0255-0857.188323] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Female genital tuberculosis (FGTB) has a profound impact on the reproductive health of patients including infertility. Conventional diagnostic techniques have low sensitivity and specificity as well as long turnaround time. There is a need of developing newer, rapid and practically adaptable technique, especially in low-income countries. OBJECTIVE To standardize and evaluate loop-mediated isothermal amplification (LAMP) technique for diagnosis of FGTB. METHODS A total of 300 endometrial biopsy samples from infertile females were subjected to Ziehl-Neelsen (ZN) staining, Lowenstein-Jensen culture, automated culture (BACTEC mycobacterial growth indicator tube), histopathological examination (HPE), nucleic acid amplification by polymerase chain reaction (PCR) and LAMP technique. Composite gold standard (either smear/culture/HPE/PCR positive) was considered for calculation of outcome parameters. RESULTS The observed sensitivities of ZN smear, culture, HPE, PCR and LAMP were 2.94%, 10.29%, 8.82%, 95.59% and 66.18%, respectively. Overall concordance between PCR and LAMP was 63%, which shows a good agreement. CONCLUSION This study is the first to evaluate LAMP in the diagnosis of FGTB and found it to be a rapid and convenient technique, especially in low resource endemic settings.
Collapse
Affiliation(s)
- S Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - L Dhaliwal
- Department of Obstetrics and Gynaecology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - P Dey
- Department of Cytology and Gynaecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - H Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - R Yadav
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - S Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
29
|
Sharma K, Sharma M, Batra N, Sharma A, Dhillon MS. Diagnostic potential of multi-targeted LAMP (loop-mediated isothermal amplification) for osteoarticular tuberculosis. J Orthop Res 2017; 35:361-365. [PMID: 27175946 DOI: 10.1002/jor.23293] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/06/2016] [Indexed: 02/04/2023]
Abstract
Delay in diagnosing osteoarticular tuberculosis (OATB) contributes significantly to morbidity by causing disfiguration and neurological sequelae. The delay caused by conventional culture and the expertise and expense involved in other nucleic acid based tests, make LAMP (loop-mediated isothermal amplification) assay a favorable middle path. We evaluated LAMP assay using IS6110 and MPB64 for rapid diagnosis of OATB by comparing with IS6110 PCR and culture. LAMP assay was performed on 140 synovial fluid and pus samples (10 culture-positive proven cases, 80 culture-negative probable cases, and 50 negative controls) using three set of primer pairs each for IS6110 and MPB64. LAMP assay, using two-target approach, had an overall sensitivity and specificity of 90% and 100% in detecting OATB. Sensitivity of IS6110 PCR, IS6110 LAMP, and MPB64 LAMP was 80%, 100%, and 100%, respectively, for confirmed cases and 72.5%, 81.75%, and 86.25%, respectively, for probable cases. Six additional cases were picked using two-target approach. LAMP assay utilizing IS6110 and MPB64 is a cost-effective technique for an early and reliable diagnosis of OATB. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:361-365, 2017.
Collapse
Affiliation(s)
- Kusum Sharma
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Megha Sharma
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Nitya Batra
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Aman Sharma
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Mandeep Singh Dhillon
- Department of Orthopaedics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
30
|
Sharma M, Sharma K, Sharma A, Gupta N, Rajwanshi A. Loop-mediated isothermal amplification (LAMP) assay for speedy diagnosis of tubercular lymphadenitis: The multi-targeted 60-minute approach. Tuberculosis (Edinb) 2016; 100:114-117. [DOI: 10.1016/j.tube.2016.07.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/13/2016] [Accepted: 07/23/2016] [Indexed: 11/25/2022]
|
31
|
Ou X, Wang S, Dong H, Pang Y, Li Q, Xia H, Qu Y, Zhang Z, Li J, Zhang J, Huan S, Chin DP, Zhao Y. Multicenter evaluation of a real-time loop-mediated isothermal amplification (RealAmp) test for rapid diagnosis of Mycobacterium tuberculosis. J Microbiol Methods 2016; 129:39-43. [PMID: 27425377 DOI: 10.1016/j.mimet.2016.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022]
Abstract
The real-time loop-mediated isothermal amplification (RealAmp) test is a novel technology for rapid diagnosis of Mycobacterium tuberculosis (MTB) from sputum samples. This test has not previously been effectively evaluated. In this study, we assessed the performance of the RealAmp test for tuberculosis (TB) detection among TB suspected patients from three provincial hospitals in China. Each eligible TB suspected patients in Shanghai, Guangzhou, and Shandong provided one sputum specimen each, smear microscopy, liquid culture, and the RealAmp test were performed per patient. A total of 1583 TB suspected patients were enrolled in the study, and 1519 were used for the performance analysis. The sensitivity and specificity of the RealAmp test for MTB detection were calculated using liquid culture as reference method. The sensitivity of RealAmp test in smear-negative and culture-positive patients was 60.08%; the sensitivity in smear-positive and culture-positive patients was 97.09%; and the overall sensitivity in culture-positive patients was 74.88%. The specificity of RealAmp test for MTB detection was 86.50%.
Collapse
Affiliation(s)
- Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | | | - Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiang Li
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yan Qu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | | | | | | | - Shitong Huan
- Bill & Melinda Gates Foundation, China Office, Beijing, China
| | - Daniel P Chin
- Bill & Melinda Gates Foundation, China Office, Beijing, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| |
Collapse
|
32
|
Bojang AL, Mendy FS, Tientcheu LD, Otu J, Antonio M, Kampmann B, Agbla S, Sutherland JS. Comparison of TB-LAMP, GeneXpert MTB/RIF and culture for diagnosis of pulmonary tuberculosis in The Gambia. J Infect 2016; 72:332-7. [DOI: 10.1016/j.jinf.2015.11.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/27/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
|
33
|
Yan L, Xiao H, Zhang Q. Systematic review: Comparison of Xpert MTB/RIF, LAMP and SAT methods for the diagnosis of pulmonary tuberculosis. Tuberculosis (Edinb) 2015; 96:75-86. [PMID: 26786658 DOI: 10.1016/j.tube.2015.11.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 09/29/2015] [Accepted: 11/17/2015] [Indexed: 11/17/2022]
Abstract
Technological advances in nucleic acid amplification have led to breakthroughs in the early detection of PTB compared to traditional sputum smear tests. The sensitivity and specificity of loop-mediated isothermal amplification (LAMP), simultaneous amplification testing (SAT), and Xpert MTB/RIF for the diagnosis of pulmonary tuberculosis were evaluated. A critical review of previous studies of LAMP, SAT, and Xpert MTB/RIF for the diagnosis of pulmonary tuberculosis that used laboratory culturing as the reference method was carried out together with a meta-analysis. In 25 previous studies, the pooled sensitivity and specificity of the diagnosis of tuberculosis were 93% and 94% for LAMP, 96% and 88% for SAT, and 89% and 98% for Xpert MTB/RIF. The I(2) values for the pooled data were >80%, indicating significant heterogeneity. In the smear-positive subgroup analysis of LAMP, the sensitivity increased from 93% to 98% (I(2) = 2.6%), and specificity was 68% (I(2) = 38.4%). In the HIV-infected subgroup analysis of Xpert MTB/RIF, the pooled sensitivity and specificity were 79% (I(2) = 72.9%) and 99% (I(2) = 64.4%). In the HIV-negative subgroup analysis for Xpert MTB/RIF, the pooled sensitivity and specificity were 72% (I(2) = 49.6%) and 99% (I(2) = 64.5%). LAMP, SAT and Xpert MTB/RIF had comparably high levels of sensitivity and specificity for the diagnosis of tuberculosis. The diagnostic sensitivity and specificity of three methods were similar, with LAMP being highly sensitive for the diagnosis of smear-positive PTB. The cost effectiveness of LAMP and SAT make them particularly suitable tests for diagnosing PTB in developing countries.
Collapse
Affiliation(s)
- Liping Yan
- Tuberculosis Clinic and Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507, Zhengmin Road, Shanghai 200433, China
| | - Heping Xiao
- Tuberculosis Clinic and Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507, Zhengmin Road, Shanghai 200433, China
| | - Qing Zhang
- Tuberculosis Clinic and Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507, Zhengmin Road, Shanghai 200433, China.
| |
Collapse
|
34
|
Beissner M, Phillips RO, Battke F, Bauer M, Badziklou K, Sarfo FS, Maman I, Rhomberg A, Piten E, Frimpong M, Huber KL, Symank D, Jansson M, Wiedemann FX, Banla Kere A, Herbinger KH, Löscher T, Bretzel G. Loop-Mediated Isothermal Amplification for Laboratory Confirmation of Buruli Ulcer Disease-Towards a Point-of-Care Test. PLoS Negl Trop Dis 2015; 9:e0004219. [PMID: 26566026 PMCID: PMC4643924 DOI: 10.1371/journal.pntd.0004219] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/17/2015] [Indexed: 11/18/2022] Open
Abstract
Background As the major burden of Buruli ulcer disease (BUD) occurs in remote rural areas, development of point-of-care (POC) tests is considered a research priority to bring diagnostic services closer to the patients. Loop-mediated isothermal amplification (LAMP), a simple, robust and cost-effective technology, has been selected as a promising POC test candidate. Three BUD-specific LAMP assays are available to date, but various technical challenges still hamper decentralized application. To overcome the requirement of cold-chains for transport and storage of reagents, the aim of this study was to establish a dry-reagent-based LAMP assay (DRB-LAMP) employing lyophilized reagents. Methodology/Principal Findings Following the design of an IS2404 based conventional LAMP (cLAMP) assay suitable to apply lyophilized reagents, a lyophylization protocol for the DRB-LAMP format was developed. Clinical performance of cLAMP was validated through testing of 140 clinical samples from 91 suspected BUD cases by routine assays, i.e. IS2404 dry-reagent-based (DRB) PCR, conventional IS2404 PCR (cPCR), IS2404 qPCR, compared to cLAMP. Whereas qPCR rendered an additional 10% of confirmed cases and samples respectively, case confirmation and positivity rates of DRB-PCR or cPCR (64.84% and 56.43%; 100% concordant results in both assays) and cLAMP (62.64% and 52.86%) were comparable and there was no significant difference between the sensitivity of the assays (DRB PCR and cPCR, 86.76%; cLAMP, 83.82%). Likewise, sensitivity of cLAMP (95.83%) and DRB-LAMP (91.67%) were comparable as determined on a set of 24 samples tested positive in all routine assays. Conclusions/Significance Both LAMP formats constitute equivalent alternatives to conventional PCR techniques. Provided the envisaged availability of field friendly DNA extraction formats, both assays are suitable for decentralized laboratory confirmation of BUD, whereby DRB-LAMP scores with the additional advantage of not requiring cold-chains. As validation of the assays was conducted in a third-level laboratory environment, field based evaluation trials are necessary to determine the clinical performance at peripheral health care level. Buruli ulcer disease (BUD) mainly occurs in remote rural areas of Sub-Saharan Africa, affects skin and soft tissue, and may lead to severe disabilities. Therefore, early diagnosis and treatment with antimycobacterial therapy are essential whereby the WHO recommends laboratory confirmation of 70% of the cases. As the current diagnostic gold standard (polymerase chain reaction [PCR]) is restricted to third-level laboratories, development of confirmatory point-of-care (POC) tests for BUD applicable at primary health care level has become a research priority to bring diagnosis closer to where the patients are. Loop-mediated isothermal amplification (LAMP) has been selected by the WHO as one of the promising candidate technologies for POC tests. The aim of this study was to establish and validate a LAMP assay applying lyophilized reagents which are stable at ambient temperature, thus avoiding the need for cold-chains. The results from this study suggest that the assay provides a valuable alternative to other PCR tests as currently used for laboratory confirmation of BUD.
Collapse
Affiliation(s)
- Marcus Beissner
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
- * E-mail:
| | - Richard Odame Phillips
- Komfo Anokye Teaching Hospital (KATH), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | | | - Malkin Bauer
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Kossi Badziklou
- Institut National d’Hygiène (INH), Ministère de la Santé, Lomé, Togo
| | - Fred Stephen Sarfo
- Komfo Anokye Teaching Hospital (KATH), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Issaka Maman
- Institut National d’Hygiène (INH), Ministère de la Santé, Lomé, Togo
| | - Agata Rhomberg
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Ebekalisai Piten
- Centre Hospitalier Régional Maritime (CHR-Maritime), Tsévié, Togo
| | - Michael Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Komfo Anokye Teaching Hospital (KATH), Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Kristina Lydia Huber
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Dominik Symank
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Moritz Jansson
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Franz Xaver Wiedemann
- German Leprosy and Tuberculosis Relief Association, Togo office (DAHW-T), Lomé, Togo
| | - Abiba Banla Kere
- Institut National d’Hygiène (INH), Ministère de la Santé, Lomé, Togo
| | - Karl-Heinz Herbinger
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Thomas Löscher
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Gisela Bretzel
- Department of Infectious Diseases and Tropical Medicine (DITM), University Hospital, Ludwig-Maximilians-University, Munich, Germany
| |
Collapse
|
35
|
Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. J Microbiol Methods 2015; 119:223-7. [PMID: 26554941 DOI: 10.1016/j.mimet.2015.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/04/2015] [Accepted: 11/07/2015] [Indexed: 12/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is increasingly used for point-of-care nucleic acid based diagnostics. LAMP can be monitored in real-time by measuring the increase in fluorescence of DNA binding dyes. However, there is little information comparing the effect of various fluorescent dyes on signal to noise ratio (SNR) or threshold time (Tt). This information is critical for implementation with field deployable diagnostic tools that require small, low power consumption, robust, and inexpensive optical components with reagent saving low volume reactions. In this study, SNR and Tt during real-time LAMP was evaluated with eleven fluorescent dyes. Of all dyes tested, SYTO-82, SYTO-84, and SYTOX Orange resulted in the shortest Tt, and SYTO-81 had the widest range of working concentrations. The optimized protocol detected 10 genome copies of Mycobacterium tuberculosis in less than 10 min, 10 copies of Giardia intestinalis in ~20 min, and 10 copies of Staphylococcus aureus or Salmonella enterica in less than 15 min. Results demonstrate that reaction efficiency depends on both dye type and concentration and the selected polymerase. The optimized protocol was evaluated in the Gene-Z™ device, a hand-held battery operated platform characterized via simple and low cost optics, and a multiple assay microfluidic chip with micron volume reaction wells. Compared to the more conventional intercalating dye (SYBR Green), reliable amplification was only observed in the Gene-Z™ when using higher concentrations of SYTO-81.
Collapse
|
36
|
Moon SH, Kim EJ, Tomono J, Miyamoto S, Mitarai S, Kim DW, Seki M. Detection of Mycobacterium tuberculosis complex in sputum specimens using a loop-mediated isothermal amplification assay in Korea. J Med Microbiol 2015; 64:1335-1340. [PMID: 26338293 DOI: 10.1099/jmm.0.000164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis complex (MTC), remains one of the leading causes of death in the world. In Korea, the current prevalence of multidrug-resistant TB (MDR-TB) poses a major problem. The most common method for diagnosing TB in developing countries is sputum smear microscopy; however, the sensitivity of this test is relatively low and it usually requires well-trained laboratory staff. Cultures of MTC require up to several weeks in sophisticated facilities, such as Biosafety Level 3. Effective diagnostic techniques are necessary to control TB. In Korea, we evaluated a loop-mediated isothermal amplification (LAMP) assay targeting the hspX gene (TB-hspX-LAMP) of MTC. For clinical evaluation, culture confirmation, smear microscopy and TB-hspX-LAMP were performed on 303 sputum specimens obtained from suspected TB patients in Korea. The sensitivity, specificity, positive predictive value and negative predictive value of TB-hspX-LAMP were 71.1, 98.8, 91.4 and 95.1%, respectively, compared with TB culture, which is the gold standard for diagnosis of TB. In contrast, the comparable values of smear microscopy were 24.4, 98.1, 68.8 and 88.2%, respectively. Therefore, we concluded that TB-hspX-LAMP was superior to the use of smear microscopy for the detection of MTC in sputum specimens in clinical settings in Korea.
Collapse
Affiliation(s)
- Se Hoon Moon
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea.,Korea University Medical Center Ansan Hospital, Ansan, Republic of Korea
| | - Eun Jin Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | | | | | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Bacteriology Division, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Dong Wook Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Republic of Korea.,Institute of Pharmacological Research, Hanyang University, Ansan, Republic of Korea
| | - Mitsuko Seki
- Dental Research Center, Nihon University School of Dentistry, Tokyo, Japan.,Department of Oral Health Sciences, Nihon University School of Dentistry, Tokyo, Japan
| |
Collapse
|
37
|
Jiang YS, Bhadra S, Li B, Wu YR, Milligan JN, Ellington AD. Robust strand exchange reactions for the sequence-specific, real-time detection of nucleic acid amplicons. Anal Chem 2015; 87:3314-20. [PMID: 25708458 DOI: 10.1021/ac504387c] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) of DNA is a powerful isothermal nucleic acid amplification method that can generate upward of 10(9) copies from less than 100 copies of template DNA within an hour. Unfortunately, although the amplification reactions are extremely powerful, real-time and specific detection of LAMP products remains analytically challenging. In order to both improve the specificity of LAMP detection and to make readout simpler and more reliable, we have replaced the intercalating dye typically used for monitoring in real-time fluorescence with a toehold-mediated strand exchange reaction termed one-step strand displacement (OSD). Due to the inherent sequence specificity of toehold-mediated strand exchange, the OSD reporter could successfully distinguish side products from true amplicons arising from templates corresponding to the biomedically relevant M. tuberculosis RNA polymerase (rpoB) and the melanoma-related biomarker BRAF. OSD allowed the Yes/No detection of rpoB in a complex mixture such as synthetic sputum and also demonstrated single nucleotide specificity in Yes/No detection of a mutant BRAF allele (V600E) in the presence of 20-fold more of the wild-type gene. Real-time detection of different genes in multiplex LAMP reactions also proved possible. The development of simple, readily designed, modular equivalents of TaqMan probes for isothermal amplification reactions should generally improve the applicability of these reactions and may eventually assist with the development of point-of-care tests.
Collapse
Affiliation(s)
- Yu Sherry Jiang
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sanchita Bhadra
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Bingling Li
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yuefeng Rose Wu
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - John N Milligan
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D Ellington
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
38
|
Gazi MA, Islam MR, Kibria MG, Mahmud Z. General and advanced diagnostic tools to detect Mycobacterium tuberculosis and their drug susceptibility: a review. Eur J Clin Microbiol Infect Dis 2015; 34:851-61. [DOI: 10.1007/s10096-014-2306-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/14/2014] [Indexed: 10/24/2022]
|
39
|
Costa P, Botelho A, Couto I, Viveiros M, Inácio J. Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members. Front Mol Biosci 2014; 1:16. [PMID: 25988157 PMCID: PMC4428369 DOI: 10.3389/fmolb.2014.00016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/25/2014] [Indexed: 12/03/2022] Open
Abstract
Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease.
Collapse
Affiliation(s)
- Pedro Costa
- Instituto Nacional de Investigação Agrária e Veterinária IPLisboa, Portugal
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
| | - Ana Botelho
- Instituto Nacional de Investigação Agrária e Veterinária IPLisboa, Portugal
| | - Isabel Couto
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
- Centro de Recursos Microbiológicos (CREM), Universidade Nova de LisboaCaparica, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
| | - João Inácio
- School of Pharmacy and Biomolecular Sciences, University of BrightonBrighton, UK
| |
Collapse
|
40
|
Elevated OPN, IP-10, and neutrophilia in loop-mediated isothermal amplification confirmed tuberculosis patients. Mediators Inflamm 2014; 2014:513263. [PMID: 25378811 PMCID: PMC4213984 DOI: 10.1155/2014/513263] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/21/2014] [Accepted: 09/08/2014] [Indexed: 11/24/2022] Open
Abstract
Tuberculosis (TB) is the second most common cause of death from infectious diseases and results in high socioeconomic losses to many countries. Proper diagnosis is the first step in TB eradication. To develop a rapid, simple, and accurate diagnostic TB test and to characterize the prevalence of Mycobacterium tuberculosis (MTB) genotypes and immune profiles of TB patients, a total of 37 TB patients and 30 healthy control (HC) from Metro Manila were enrolled. Loop-mediated isothermal amplification (LAMP) reliably detected MTB infection. Manila genotype was identified by spoligotyping method in all TB patients. Osteopontin (OPN), interferon-γ-induced protein 10 kDa (IP-10), and neutrophil counts were found to reflect the acute stage of MTB infection. The sensitivity and specificity were 94.6% and 93.3%, respectively, for both OPN and IP-10, and they were 83.8% and 78.6%, respectively, for neutrophils. The combination of OPN, IP-10, neutrophil count, IL-6, IL-8, TNF-α, MCP-1, platelets, galectin-9, and leukocyte count correctly identifies all the HC and 96.3% of TB patients. LAMP method may serve as a rapid, supportive method in addition to time-consuming culture methods. OPN, IP-10, and neutrophil counts are useful in detecting MTB infection and may have utility in monitoring the course of the disease.
Collapse
|
41
|
Issa R, Abdul H, Hashim SH, Seradja VH, Shaili N'A, Hassan NAM. High resolution melting analysis for the differentiation of Mycobacterium species. J Med Microbiol 2014; 63:1284-1287. [PMID: 25038139 DOI: 10.1099/jmm.0.072611-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A quantitative real-time PCR (qPCR) followed by high resolution melting (HRM) analysis was developed for the differentiation of Mycobacterium species. Rapid differentiation of Mycobacterium species is necessary for the effective diagnosis and management of tuberculosis. In this study, the 16S rRNA gene was tested as the target since this has been identified as a suitable target for the identification of mycobacteria species. During the temperature gradient and primer optimization process, the melting peak (Tm) analysis was determined at a concentration of 50 ng DNA template and 0.3, 0.4 and 0.5 µM primer. The qPCR assay for the detection of other mycobacterial species was done at the Tm and primer concentration of 62 °C and 0.4 µM, respectively. The HRM analysis generated cluster patterns that were specific and sensitive to distinguished small sequence differences of the Mycobacterium species. This study suggests that the 16S rRNA-based real-time PCR followed by HRM analysis produced unique cluster patterns for species of Mycobacterium and could differentiate the closely related mycobacteria species.
Collapse
Affiliation(s)
- Rahizan Issa
- Bacteriology Unit, Infectious Diseases Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Hatijah Abdul
- Bacteriology Unit, Infectious Diseases Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Siti Hasmah Hashim
- Bacteriology Unit, Infectious Diseases Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Valentinus H Seradja
- Bacteriology Unit, Infectious Diseases Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Nurul 'Aishah Shaili
- Bacteriology Unit, Infectious Diseases Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Nurul Akma Mohd Hassan
- Bacteriology Unit, Infectious Diseases Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| |
Collapse
|
42
|
Dhama K, Karthik K, Chakraborty S, Tiwari R, Kapoor S, Kumar A, Thomas P. Loop-mediated isothermal amplification of DNA (LAMP): a new diagnostic tool lights the world of diagnosis of animal and human pathogens: a review. Pak J Biol Sci 2014; 17:151-66. [PMID: 24783797 DOI: 10.3923/pjbs.2014.151.166] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Diagnosis is an important part in case of animal husbandry as treatment of a disease depends on it. Advancement in molecular biology has generated various sophisticated tools like Polymerase Chain Reaction (PCR), its versions along with pen-side diagnostic techniques. Every diagnostic test however has both advantages and disadvantages; PCR is not an exception to this statement. To ease the odds faced by PCR several non-PCR techniques which can amplify DNA at a constant temperature has become the need of hour, thus generating a variety of isothermal amplification techniques including Nucleic Acid Sequence-Based Amplification (NASBA) along with Self-Sustained Sequence Replication (3SR) and Strand Displacement Amplification (SDA) and Loop mediated isothermal amplification (LAMP) test. LAMP stands out to be a good and effective diagnostic test for empowering in developing countries as it does not require sophisticated equipments and skilled personnel and proves to be cost-effective. Performance of LAMP mainly relies on crafting of six primers (including 2 loop primers) ultimately accelerating the reaction. LAMP amplifies DNA in the process pyrophosphates are formed causing turbidity that facilitates visualisation in a more effective way than PCR. The Bst and Bsm polymerase are the required enzymes for LAMP that does not possess 5'-3' exonuclease activity. Results can be visualized by adding DNA binding dye, SYBR green. LAMP is more stable than PCR and real-time PCR. Non-involvement of template DNA preparation and ability to generate 10(9) copies of DNA are added benefits that make it more effective than NASBA or 3SR and SDA. Thus, it fetches researcher's interest in developing various versions of LAMP viz., its combination with lateral flow assay or micro LAMP and more recently lyophilized and electric (e) LAMP. Availability of ready to use LAMP kits has helped diagnosis of almost all pathogens. LAMP associated technologies however needs to be developed as a part of LAMP platform rather than developing them as separate entities. This review deals with all these salient features of this newly developed tool that has enlightened the world of diagnosis.
Collapse
|
43
|
Ou X, Li Q, Xia H, Pang Y, Wang S, Zhao B, Song Y, Zhou Y, Zheng Y, Zhang Z, Zhang Z, Li J, Dong H, Zhang J, Kam KM, Chi J, Huan S, Chin DP, Zhao Y. Diagnostic accuracy of the PURE-LAMP test for pulmonary tuberculosis at the county-level laboratory in China. PLoS One 2014; 9:e94544. [PMID: 24788724 PMCID: PMC4006777 DOI: 10.1371/journal.pone.0094544] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 03/17/2014] [Indexed: 01/31/2023] Open
Abstract
Background Early and effective detection of Mycobacterium tuberculosis (MTB), particularly in smear-negative tuberculosis (TB), is a priority for global TB control. Loop-mediated isothermal amplification with a procedure for ultra rapid DNA extraction (PURE-LAMP) can detect TB in sputum samples rapidly and with high sensitivity and specificity. However, the PURE-LAMP test has not been effectively evaluated, especially in resource-limited laboratories. In this study, we evaluated the performance of the PURE-LAMP test for TB detection in TB suspects from two county-level TB dispensaries in China. Methodology/Principal Findings From April 2011 to February 2012, patients with suspected TB were continuously enrolled from two county-level TB laboratories in China. Three sputum samples (spot, night, and morning sputum) were collected from each recruited patient. Detection of MTB by PURE-LAMP was compared to a reference standard L-J culture. The results showed that the sensitivity of the PURE-LAMP test based on spot sputum for MTB detection was 70.67%, while the sensitivity of the PURE-LAMP test based on spot sputum for MTB detection in smear positive and culture positive patients and smear negative and culture positive patients was 92.12% and 53.81%, respectively. The specificity of PURE-LAMP based on spot sputum for MTB detection was 98.32%. The sensitivity and specificity of the PURE-LAMP test based on three sputa combination for MTB detection was 88.80% and 96.86%, respectively. The results also showed that the PURE-LAMP test had a significantly lower contamination rate than did solid culture. Conclusions/Significance The study suggested that, in peripheral-level TB laboratories in China, the PURE-LAMP test showed high sensitivity and specificity for TB detection in TB suspects, making it a more effective, rapid, and safe method worthy of broader use in the future.
Collapse
Affiliation(s)
- Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Qiang Li
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Yuanyuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Yang Zheng
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
| | - Zhijian Zhang
- Respiratory Diseases Department of Nanlou, Chinese People’s Liberation Army General Hospital, Beijing, P. R. China
| | | | | | | | | | - Kai Man Kam
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Junying Chi
- Bill & Melinda Gates Foundation, China Office, Beijing, China
| | - Shitong Huan
- Bill & Melinda Gates Foundation, China Office, Beijing, China
| | - Daniel P. Chin
- Bill & Melinda Gates Foundation, China Office, Beijing, China
- * E-mail: (Y. Zhao); (DPC)
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, P. R. China
- * E-mail: (Y. Zhao); (DPC)
| |
Collapse
|
44
|
Development and clinical evaluation of sdaA loop-mediated isothermal amplification assay for detection of Mycobacterium tuberculosis with an approach to prevent carryover contamination. J Clin Microbiol 2014; 52:2662-4. [PMID: 24789191 DOI: 10.1128/jcm.00907-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A rapid and sensitive loop-mediated isothermal amplification assay for the sdaA gene of Mycobacterium tuberculosis was developed using a dUTP-uracil-N-glycosylase (dUTP-UNG) strategy to prevent carryover contamination. Evaluation of the assay using clinical specimens (n = 648) showed high specificity (97.2%) and sensitivity (100%), demonstrating its potential as a diagnostic test for tuberculosis, especially in resource-limited settings.
Collapse
|
45
|
Yuan LY, Li Y, Wang M, Ke ZQ, Xu WZ. Rapid and effective diagnosis of pulmonary tuberculosis with novel and sensitive loop-mediated isothermal amplification (LAMP) assay in clinical samples: A meta-analysis. J Infect Chemother 2014; 20:86-92. [DOI: 10.1016/j.jiac.2013.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 06/24/2013] [Accepted: 07/25/2013] [Indexed: 11/29/2022]
|
46
|
Sethi S, Sethi SK, Singh S, Dhatwalia SK, Yadav R, Mewara A, Singh M, Tewari R, Sharma M. Evaluation of in-house loop-mediated isothermal amplification (LAMP) assay for rapid diagnosis of M. tuberculosis in pulmonary specimens. J Clin Lab Anal 2014; 27:272-6. [PMID: 23852783 DOI: 10.1002/jcla.21596] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 02/04/2013] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Loop-mediated isothermal amplification (LAMP) assay has come forward as a rapid, cost-effective molecular technique for diagnosis of tuberculosis (TB) in developing countries. This study evaluated Mycobacterium tuberculosis-specific in-house LAMP assay targeting 16s rRNA and compared it with other conventional tests and nucleic acid amplification assay (IS6110 PCR). METHODS A total of 133 sputum specimens (103 from suspected pulmonary TB cases and 30 from non-TB controls) were subjected to conventional tests, IS6110 PCR and 16s rRNA LAMP assay. RESULTS Of the 103 patients, the maximum number of cases were found to be positive by LAMP assay, that is, in 87 (84.5%) patients, followed by culture positive in 78 (75.7%), IS6110 PCR in 74 (71.8%), and smear positive in 70 (67.9%) patients. Of the 83 smear positive and/or culture positive cases, LAMP detected 77 (92.77%) cases, and was found to be superior to IS6110 PCR, which could detect 69 (83.1%) cases; a concordance of 0.6 was obtained between the two tests using kappa statistics. CONCLUSION Overall, LAMP was simple and efficacious for early diagnosis of smear positive, culture positive cases as well as for confirmation of smear negative, culture negative cases, and was found to be superior to IS6110 PCR.
Collapse
Affiliation(s)
- Sunil Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | - Sunil Kumar Sethi
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Chegou NN, Hoek KGP, Kriel M, Warren RM, Victor TC, Walzl G. Tuberculosis assays: past, present and future. Expert Rev Anti Infect Ther 2014; 9:457-69. [DOI: 10.1586/eri.11.23] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
48
|
Phetsuksiri B, Rudeeaneksin J, Srisungngam S, Bunchoo S, Roienthong D, Mukai T, Nakajima C, Hamada S, Suzuki Y. Applicability of in-house loop-mediated isothermal amplification for rapid identification of Mycobacterium tuberculosis complex grown on solid media. Jpn J Infect Dis 2013; 66:249-51. [PMID: 23698490 DOI: 10.7883/yoken.66.249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A simple, rapid, and low-cost identification method is required in tuberculosis high-burden countries. We report the applicability of in-house loop-mediated isothermal amplification (LAMP) targeting 16S ribosomal RNA for the rapid identification of Mycobacterium tuberculosis complex grown on Lowenstein-Jensen media. Eighty acid-fast staining-positive clinical isolates were selected and used to evaluate the LAMP assay in comparison with polymerase chain reaction and conventional culture-based tests. The LAMP assay identified 60 M. tuberculosis isolates from 80 clinical isolates using simple heat-extracted DNA directly from the colony suspension. The results were in complete agreement with those obtained using the other methods, and the utility of the direct LAMP assay from a colony was demonstrated. The LAMP assay appears to be a practical and low-cost method that can be used for the rapid identification of M. tuberculosis isolates and suitable for endemic low-resource settings.
Collapse
Affiliation(s)
- Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Wilson ML. Rapid Diagnosis of Mycobacterium tuberculosis Infection and Drug Susceptibility Testing. Arch Pathol Lab Med 2013; 137:812-9. [DOI: 10.5858/arpa.2011-0578-ra] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—The global control of tuberculosis remains a challenge from the standpoint of diagnosis, detection of drug resistance, and treatment. This is an area of special concern to the health of women and children, particularly in regions of the world with high infant mortality rates and where women have limited access to health care.
Objective.—Because treatment can only be initiated when infection is detected, and is guided by the results of antimicrobial susceptibility testing, there recently has been a marked increase in the development and testing of novel assays designed to detect Mycobacterium tuberculosis complex, with or without simultaneous detection of resistance to isoniazid and/or rifampin. Both nonmolecular and molecular assays have been developed. This review will summarize the current knowledge about the use of rapid tests to detect M tuberculosis and drug resistance.
Data Sources.—Review of the most recent World Health Organization Global Tuberculosis Report, as well as selected publications in the primary research literature, meta-analyses, and review articles.
Conclusions.—To a large extent, nonmolecular methods are refinements or modifications of conventional methods, with the primary goal of providing more rapid test results. In contrast, molecular methods use novel technologies to detect the presence of M tuberculosis complex and genes conferring drug resistance. Evaluations of molecular assays have generally shown that these assays are of variable sensitivity for detecting the presence of M tuberculosis complex, and in particular are insensitive when used with smear-negative specimens. As a group, molecular assays have been shown to be of high sensitivity for detecting resistance to rifampin, but of variable sensitivity for detecting resistance to isoniazid.
Collapse
Affiliation(s)
- Michael L. Wilson
- From the Department of Pathology and Laboratory Services, Denver Health, Denver, Colorado; and the Department of Pathology, University of Colorado School of Medicine, Aurora
| |
Collapse
|
50
|
Aryan E, Makvandi M, Farajzadeh A, Huygen K, Alvandi AH, Gouya MM, Sadrizadeh A, Romano M. Clinical value of IS6110-based loop-mediated isothermal amplification for detection of Mycobacterium tuberculosis complex in respiratory specimens. J Infect 2013; 66:487-93. [DOI: 10.1016/j.jinf.2013.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/08/2013] [Accepted: 02/16/2013] [Indexed: 12/01/2022]
|