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Wen XH, Han YL, Cao XS, Zhao W, Yan Z, Yan L, Wen JX, Hu ZD, Zheng WQ. Diagnostic value of nucleic acid amplification tests for tuberculous pleural effusion. Future Microbiol 2023; 18:971-983. [PMID: 37702019 DOI: 10.2217/fmb-2023-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
Diagnosing tuberculous pleural effusion (TPE) is challenging for pulmonologists and laboratory scientists. The gold standards for TPE diagnosis are pleural fluid Ziehl-Neelsen staining, Mycobacterium tuberculosis (Mtb) culture and pleural biopsy. These tools have limitations, including low sensitivity, long turnaround time and invasiveness. The nucleic acid amplification test (NAAT) is a rapid and minimally invasive tool for diagnosing TPE. This review summarizes the diagnostic accuracy of available NAATs for TPE, with a focus on the evidence from systematic reviews and meta-analyses. The NAATs summarized in this review include in-house NAATs, GeneXpert-MTB/RIF, GeneXpert-MTB/RIF Ultra, simultaneous amplification and testing-tuberculosis, FluoroType MTB and loop-mediated isothermal amplification.
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Affiliation(s)
- Xu-Hui Wen
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
- Department of Parasitology, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Yu-Ling Han
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
- Department of Parasitology, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Xi-Shan Cao
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Wen Zhao
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Zhi Yan
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
- Department of Parasitology, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Li Yan
- Department of Respiratory & Critical Care Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Jian-Xun Wen
- Department of Medical Experiment Center, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
| | - Zhi-De Hu
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
| | - Wen-Qi Zheng
- Department of Laboratory Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot, 010010, China
- Department of Parasitology, Basic Medical Sciences College of Inner Mongolia Medical University, Hohhot, 010050, China
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Meregildo-Rodriguez ED, Asmat-Rubio MG, Vásquez-Tirado GA. Droplet digital PCR vs. quantitative real time-PCR for diagnosis of pulmonary and extrapulmonary tuberculosis: systematic review and meta-analysis. Front Med (Lausanne) 2023; 10:1248842. [PMID: 37608829 PMCID: PMC10440704 DOI: 10.3389/fmed.2023.1248842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
Tuberculosis is a rising global public health emergency. Then, it is a priority to undertake innovations in preventive, diagnostic, and therapeutic methods. Improved diagnostic methods for tuberculosis are urgently needed to address this global epidemic. These methods should be rapid, accurate, affordable, and able to detect drug-resistant tuberculosis. The benefits of these new diagnostic technics include earlier diagnosis and treatment, improved patient outcomes, and reduced economic burden. Therefore, we aimed to systematically review the diagnostic performance of droplet digital PCR (ddPCR)-a third-generation PCR-compared with quantitative Real Time-PCR (qPCR) for diagnosing pulmonary and extrapulmonary tuberculosis. We included 14 diagnostic accuracy test studies performed in Asia, Europe, and Latin America, 1,672 participants or biological samples, and 975 events (pulmonary or extrapulmonary tuberculosis). Most of the included studies had a low risk of bias (QUADAS-C tool). Sensitivity and specificity were lower for ddPCR [0.56 (95% CI 0.53-0.58) and 0.97 (95% CI 0.96-0.98), respectively] than for qPCR [0.66 (95% CI 0.60-0.71) and 0.98 (95% CI 0.97-0.99), respectively]. However, the area under the ROC curve (AUC) was higher for ddPCR than for qPCR (0.97 and 0.94, respectively). Comparing both AUCs using the Hanley & McNeil method, we found statistically significant differences (AUC difference of 4.40%, p = 0.0020). In the heterogeneity analysis, we found significant differences between both techniques according to the continent of origin of the study and the location of tuberculosis (pulmonary or extrapulmonary disease). The AUCs of both methods were similar in pulmonary tuberculosis. However, for extrapulmonary tuberculosis, the AUC was higher for ddPCR. We found some limitations: (1) significant heterogeneity of the studies, and (2) we could not perform subgroup analyses according to other relevant variables, such as the age and sex of the participants. Nonetheless, this study is the first meta-analysis that shows that ddPCR has a comparable diagnostic performance than qPCR for pulmonary tuberculosis. However, for extrapulmonary tuberculosis, ddPCR has a better discriminant capacity to differentiate between patients with and without extrapulmonary tuberculosis. We conclude that ddPCR is likely the best diagnostic technic for tuberculosis diagnosis, especially for extrapulmonary tuberculosis. More studies are still needed yet. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022382768, CRD42022382768.
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Kechin A, Oscorbin I, Cherednichenko A, Khrapov E, Schwartz Y, Stavitskaya N, Filipenko M. Selection of IS6110 conserved regions for the detection of Mycobacterium tuberculosis using qPCR and LAMP. Arch Microbiol 2023; 205:71. [PMID: 36688992 DOI: 10.1007/s00203-023-03410-5] [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: 08/24/2022] [Revised: 11/27/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
IS6110 insertion sequence is a frequently used target for Mycobacterium tuberculosis detection. However, its sequence variability is studied insufficiently. We aimed to identify the most conservative and variable regions in IS6110 sequences and develop qPCR and LAMP oligonucleotide sets for the conservative regions. Using in-house Python scripts, 3609 M. tuberculosis genome sequences from the NCBI database were aligned; conservative regions were identified to design oligonucleotide sets. IS6110 fragments located within the 31-231 bp region were the most conservative and represented in genomes and were used to design qPCR and LAMP oligonucleotides. The in silico sensitivity of the qPCR oligonucleotides on the whole genome set was 99.1% and 98.4%. For the LAMP primers developed, the sensitivity was 96.9%. For qPCR, the limit of detection with 95% confidence (LoD95%) was four IS6110 copies per reaction, with LoD90% being 200 BCG cells per ml of artificial sputum. For LAMP, LoD95% was 16 copies per reaction, with LoD90% being 400 Mycobacterium bovis Bacille Calmette-Guerin (BCG) cells per ml of artificial sputum. We have demonstrated the IS6110 sequence variability and designed highly sensitive qPCR and LAMP oligonucleotides to detect M. tuberculosis.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation.
| | - Igor Oscorbin
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
| | - Andrey Cherednichenko
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
| | - Yakov Schwartz
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Nataliya Stavitskaya
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Maksim Filipenko
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
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PCR-free electrochemical genosensor for Mycobacterium tuberculosis complex detection based on two-dimensional Ti3C2 Mxene-polypyrrole signal amplification. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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5
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Fan Y, Chen J, Liu M, Xu X, Zhang Y, Yue P, Cao W, Ji Z, Su X, Wen S, Kong J, Zhou G, Li B, Dong Y, Liu A, Bao F. Application of Droplet Digital PCR to Detection of Mycobacterium tuberculosis and Mycobacterium leprae Infections: A Narrative Review. Infect Drug Resist 2022; 15:1067-1076. [PMID: 35313727 PMCID: PMC8934166 DOI: 10.2147/idr.s349607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (MTB) infection, which has seriously endangered human health for many years. With the emergence of multidrug-resistant and extensively drug-resistant MTB, the prevention and treatment of TB has become a pressing need. Early diagnosis, drug resistance monitoring, and control of disease transmission are critical aspects in the prevention and treatment of TB. However, the currently available diagnostic technologies and drug sensitivity tests are time consuming, and thus, it is difficult to achieve the goal of early diagnosis and detection drug sensitivity, which results in limited control of disease transmission. The development of molecular testing technology has gradually achieved the vision of rapid and accurate diagnosis of TB. Droplet digital PCR (ddPCR) is an excellent nucleic acid quantification method with high sensitivity and no need for a calibration curve. Herein, we review the application of ddPCR in TB diagnosis and drug resistance detection and transmission monitoring.
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Affiliation(s)
- Yuxin Fan
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Jingjing Chen
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Meixiao Liu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Xin Xu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Yu Zhang
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Peng Yue
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Wenjing Cao
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Zhenhua Ji
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Xuan Su
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Shiyuan Wen
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Jing Kong
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Guozhong Zhou
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Bingxue Li
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Yan Dong
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Aihua Liu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Correspondence: Aihua Liu; Fukai Bao, The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China, Email ;
| | - Fukai Bao
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
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Development and Validation of Signature Sequence-Based PCR for Improved Molecular Diagnosis of Tuberculosis. J Mol Diagn 2021; 23:1138-1144. [PMID: 34116244 DOI: 10.1016/j.jmoldx.2021.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 05/13/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022] Open
Abstract
Reliable, fast, and affordable diagnosis for tuberculosis (TB) remains a challenge to reduce disease incidence in resource-poor countries. Tests based on nucleotide sequences that are signature to Mycobacterium tuberculosis have the potential to make a positive impact on case detection rates, which can eventually help control TB. Using extensive comparative bioinformatics approach, we mined the genome for M. tuberculosis-specific genes and identified four genes so-called signature sequence (SS). With <25% homology with other known genes/proteins of mycobacterial/nonmycobacterial origin in various databases, these SS genes are ideal targets for species-specific identification. Sputum from suspected patients was liquefied using novel complete liquefying reagent, and DNA was isolated. Samples from patients (n = 417), reporting to TB clinics at two different hospitals, which met our inclusion criteria, were collected for this study. A small number (n = 143) was used for initial standardization, and the remaining patient samples (n = 274) were evaluated by SS and compared with smear microscopy, GeneXpert, culture, and clinical outcome. An overwhelming sensitivity of 97.0%, significantly higher than GeneXpert (95.0%), was seen. SS could pick all smear-negative, but culture-positive samples, along with other culture-negative samples; some of the latter were declared clinically positive. Our results yielded superior sensitivity and specificity through conventional PCR.
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Stellmacher F, Kirfel J, Kalsdorf B, Maurer FP, Perner S, Goldmann T. [Molecular pathology of tuberculosis : Status, methodology, and limits]. DER PATHOLOGE 2021; 42:78-82. [PMID: 33475809 DOI: 10.1007/s00292-021-00911-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 11/24/2022]
Abstract
In the diagnosis of mycobacterioses, microbiological examination with culture and antibiogram, possibly in combination with molecular biological testing of the fresh material, still represents the gold standard. However, these methods are not available for formalin-fixed paraffin-embedded (FFPE) material or other fixed samples. For this reason, the first step in pathology is to attempt microscopic pathogen detection (ZN/Fite/rhodamine-auramine). Subsequently, molecular pathological examination for the detection of mycobacterial gene sequences should also be considered mandatory today. Although this has clear limits due to the material, it is nevertheless well suited, if carried out correctly, to detect a mycobacterial infection or make it unlikely. A negative result may favor an alternative diagnosis but does not completely rule out mycobacteriosis.For the therapy of tuberculosis or nontuberculous mycobacterial (NTM) disease, the reliable detection of the species and the determination of resistance is of utmost importance. With regard to therapy, the clinician cannot afford to make a false diagnosis. In case of doubt, a rebiopsy for sampling native material, particularly for microbiological testing, should be discussed.
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Affiliation(s)
- F Stellmacher
- Pathologie, Forschungszentrum Borstel, Leibniz Lungenzentrum, Parkallee 1-40, 23845, Borstel, Deutschland.
| | - J Kirfel
- Institut für Pathologie, Universitätsklinikum Schleswig-Holstein, 23538, Lübeck, Deutschland
| | - B Kalsdorf
- Medizinische Klinik Borstel, Leibniz Lungenzentrum, Borstel, Deutschland.,Exzellenzcluster Precision Medicine in Chronic Inflammation, Kiel, Deutschland
| | - F P Maurer
- Nationales und WHO Supranationales Referenzzentrum für Mykobakterien, Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Deutschland.,Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - S Perner
- Pathologie, Forschungszentrum Borstel, Leibniz Lungenzentrum, Parkallee 1-40, 23845, Borstel, Deutschland.,Institut für Pathologie, Universitätsklinikum Schleswig-Holstein, 23538, Lübeck, Deutschland
| | - T Goldmann
- Pathologie, Forschungszentrum Borstel, Leibniz Lungenzentrum, Parkallee 1-40, 23845, Borstel, Deutschland
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Response surface methodology optimized electrochemical DNA biosensor based on HAPNPTs/PPY/MWCNTs nanocomposite for detecting Mycobacterium tuberculosis. Talanta 2021; 226:122099. [PMID: 33676656 DOI: 10.1016/j.talanta.2021.122099] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/26/2020] [Accepted: 01/05/2021] [Indexed: 01/27/2023]
Abstract
An important issue in the prognosis of tuberculosis (TB) is a short period between correct diagnosis and start the suitable antibiotic therapy. So, a rapid and valid method for detection of Mycobacterium tuberculosis (M. tb) complex is considered as a necessity. Herein, a rapid, low-cost, and PCR-free DNA biosensor was developed based on multi-walled carbon nanotubes (MWCNTs), polypyrrole (PPy), and hydroxyapatite nanoparticles (HAPNPs) for highly sensitive and specific recognition of M.tb. The biosensor consisted of M.tb ssDNA probe covalently attached to the HANPs/PPy/MWCNTs/GCE surface that hybridized to a complementary target sequence to form a duplex DNA. The M.tb target recognition was based on the oxidation signal of the electroactive Methylene Blue (MB) on the surface of the modified GCE using differential pulse voltammetry (DPV) method. It is worth to mention that for the first time Plackett-Burman (PB) screening design and response surface method (RSM) based on central composite design (CCD) was applied as a powerful and an efficient approach to find optimal conditions for maximum M.tb biosensor performance leading to simplicity and rapidity of operation. The proposed DNA biosensor exhibits a wide detection range from 0.25 to 200.0 nM with a low detection limit of 0.141 nM. The performance of designed biosensor for clinical diagnosis and practical applications was revealed through hybridization between DNA probe-modified GCE and extracted DNA from sputum clinical samples.
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Demonstration of a fast and easy sample-to-answer protocol for tuberculosis screening in point-of-care settings: A proof of concept study. PLoS One 2020; 15:e0242408. [PMID: 33315885 PMCID: PMC7735633 DOI: 10.1371/journal.pone.0242408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/03/2020] [Indexed: 11/22/2022] Open
Abstract
We sought to develop a smooth and low cost sample preparation and DNA extraction protocol, streamlined with a ready-to-use qPCR in a portable instrument to overcome some of the existing hurdles. Several solutions were evaluated as to their ability to liquefy a mucin-based matrix. Each liquefied matrix, supplemented with either Mycobacterium tuberculosis (MTB) H37Rv strain DNA or intact cells, was aliquoted onto a filter paper embedded with solubilizing agents, and was subsequently dried up. Most of the nucleic acids, including genomic DNA from the bacilli and the host, binds to the filter paper. Next, several protocols were evaluated to elute the DNA from the paper, using qPCR to detect the insertion sequence IS6110, a M. tuberculosis complex genomic marker. The limit of detection (LOD) of the best protocol was then evaluated using parallel seeding and colony counting. The protocol was also evaluated using seventeen sputum samples, previously characterized by the GeneXpert or culture. Two instruments (the ABI7500 Standard and the Q3-Plus system) and two reagents storage formats (frozen or ready-to-use) were evaluated. Solutions containing guanidine isothiocyanate exerted the best liquefying effect on the mucin-based matrix extracted from one 6-mm punches, followed by a brief incubation at 95°C. The resulting DNA contained impurities, but a simple 1:10 dilution elicited the detection of MTB and human genomic targets. The described protocol presented an apparent LOD of 02 CFU/mL of MTB. Challenging the protocol with previously characterized samples showed substantial agreement with GeneXpert MTB/RIF results (sensitivity of 90%, agreement of 88.9%, kappa coefficient of 0.77), and moderate agreement with culture results (sensitivity of 100%, agreement of 78.9%, kappa coefficient of 0.58). This work presents a sensitive proof–of-concept protocol for sputum liquefaction and decontamination followed by a simple DNA extraction procedure, in which the extraction steps are streamlined with a ready-to-use qPCR in a portable instrument that can be employed in low infrastructure settings.
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Salimiyan Rizi K, Aryan E, Meshkat Z, Ranjbar G, Sankian M, Ghazvini K, Farsiani H, Pourianfar HR, Rezayi M. The overview and perspectives of biosensors and Mycobacterium tuberculosis: A systematic review. J Cell Physiol 2020; 236:1730-1750. [PMID: 32930412 DOI: 10.1002/jcp.30007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/01/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) is referred to as a "consumption" or phthisis, which has been a fatal human disease for thousands of years. Mycobacterium tuberculosis (M. tb) might have been responsible for the death of more humans than any other bacterial pathogens. Therefore, the rapid diagnosis of this bacterial infection plays a pivotal role in the timely and appropriate treatment of the patients, as well as the prevention of disease spread. More than 98% of TB cases are reported in developing countries, and due to the lack of well-equipped and specialized diagnostic laboratories, development of effective diagnostic methods based on biosensors is essential for this bacterium. In this review, original articles published in English were retrieved from multiple databases, such as PubMed, Scopus, Google Scholar, Science Direct, and Cochrane Library during January 2010-October 2019. In addition, the reference lists of the articles were also searched. Among 109 electronically searched citations, 42 articles met the inclusion criteria. The highest potential and wide usage of biosensors for the diagnosis of M. tb and its drug resistance belonged to DNA electrochemical biosensors (isoniazid and rifampin strains). Use of biosensors is expanding for the detection of resistant strains of anti-TB antibiotics with high sensitivity and accuracy, while the speed of these sensory methods is considered essential as well. Furthermore, the lowest limit of detection (0.9 fg/ml) from an electrochemical DNA biosensor was based on graphene-modified iron-oxide chitosan hybrid deposited on fluorine tin oxide for the MPT64 antigen target. According to the results, the most common methods used for M. tb detection include acid-fast staining, cultivation, and polymerase chain reaction (PCR). Although molecular techniques (e.g., PCR and real-time PCR) are rapid and sensitive, they require sophisticated laboratory and apparatuses, as well as skilled personnel and expertise in the commentary of the results. Biosensors are fast, valid, and cost-efficient diagnostic method, and the improvement of their quality is of paramount importance in resource-constrained settings.
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Affiliation(s)
- Kobra Salimiyan Rizi
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Aryan
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Golnaz Ranjbar
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Sankian
- Division of Immunobiochemistry, Immunology Research Centre, Bu-Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hadi Farsiani
- Department of Medical Bacteriology and Virology, School of Medicine, Antimicrobial Resistance Research Center, Qaem University Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid R Pourianfar
- Research Department of Industrial Fungi Biotechnology, Research Institute for Industrial Biotechnology, Academic Centre for Education, Culture and Research [ACECR]-Khorasan Razavi Province Branch, Mashhad, Iran
| | - Majid Rezayi
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology and Nanotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Bello GL, Morais FCL, Wolf JM, Gehlen M, Soares TDS, Halon ML, Barcellos RB, Rossetti MLR. Improvement of Mycobacterium tuberculosis detection in sputum using DNA extracted by sonication. Braz J Infect Dis 2020; 24:398-404. [PMID: 32931759 PMCID: PMC9392136 DOI: 10.1016/j.bjid.2020.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/11/2020] [Accepted: 08/16/2020] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB) is one of the infectious diseases with high mortality in the world. DNA amplification techniques have been used to overcome barriers to the diagnosis of this disease. However, the success of these methodologies is highly dependent on the DNA obtained from the sample. This study was carried out to verify whether the DNA extracted by sonication (in house method) could yield suitable DNA for amplification by real-time PCR (qPCR). Sixty sputum samples were submitted to DNA extraction using sonication compared to a commercial method (Detect-TB kit, Labtest/MG-Brazil). All DNA samples were amplified by qPCR for IS6110 region (IS6110-qPCR/SYBR Green assay). Out of 60 samples, 40 were positive for TB; of these, all had positive results when extracted by sonication (100%) and 80% when extracted by the commercial method. The limit of detection (LOD) of Mycobacterium tuberculosis (H37Rv strain) by qPCR was 14 CFU/mL when the DNA was extracted by sonication, compared to countless colonies when extracted by commercial kit. In conclusion, the sonication protocol (without purification step) proved to be a simple, fast, and suitable method for obtaining DNA for use in qPCR from sputum samples.
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Affiliation(s)
- Graziele Lima Bello
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil
| | - Franciele Costa Leite Morais
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil
| | - Jonas Michel Wolf
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil
| | - Mirela Gehlen
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Pneumologia, Porto Alegre, RS, Brasil
| | | | - Maria Laura Halon
- Secretaria do Estado do Rio Grande do Sul (SES/ RS), Centro de Desenvolvimento Científico e Tecnológico (CDCT), Porto Alegre, RS, Brasil
| | - Regina Bones Barcellos
- Secretaria do Estado do Rio Grande do Sul (SES/ RS), Centro de Desenvolvimento Científico e Tecnológico (CDCT), Porto Alegre, RS, Brasil; Universidade Federal do Rio de Janeiro (UFRJ), Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil
| | - Maria Lucia Rosa Rossetti
- Universidade Luterana do Brasil (ULBRA), Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil; Universidade Federal do Rio de Janeiro (UFRJ), Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil.
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Kalaiarasan E, Thangavelu K, Krishnapriya K, Muthuraj M, Jose M, Joseph NM. Diagnostic performance of real time PCR and MALDI-TOF in the detection of nontuberculous mycobacteria from clinical isolates. Tuberculosis (Edinb) 2020; 125:101988. [PMID: 32916384 DOI: 10.1016/j.tube.2020.101988] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 02/07/2023]
Abstract
This study aimed to evaluate the performance of real-time PCR (qPCR) and MALDI-TOF for accurate and timely detection of nontuberculous mycobacterium (NTM) from clinical isolates. We collected fifty NTM suspected Mycobacteria Growth Indicator Tube (MGIT) cultures and analysed the diagnostic performance of qPCR and VITEK MS using Line Probe Assay (LPA) GenoType CM (Common Mycobacteria) as gold standard. The qPCR assays targeting 16S rRNA, ITS and IS6110 genes were developed for the identification of NTM and Mycobacterium tuberculosis complex (MTBC). LPA GenoType CM, a PCR technique targeting 23S rRNA gene, followed by reverse hybridization and line probe technology identified 90% of Mycobacterium species including M. fortuitum (16%,n = 8), M. intracellulare (10%,n = 5), M. gordonae (10%,n = 5), M. xenopi (4%,n = 2), M. scrofulaceum (4%,n = 2), Mycobacterium additional species (AS) (32%,n = 16) and MTBC (14%,n = 7), qPCR detected 80% of Mycobacterium species (NTM, 66% (n = 33) and MTBC, 14% (n = 7)) and MALDI-TOF, 52% (M. fortuitum (12%,n = 6), M. intracellulare (10%, n = 5), M. simiae (8%,n = 4), M. gordonae (8%,n = 4), and MTBC (14%,n = 7)). Sensitivity of qPCR and MALDI-TOF was 88.9% and 57.8%, respectively with 100% specificity. The combination of qPCR and MALDI-TOF remains an appropriate test for timely diagnosis of Mycobacterium species. This may eventually assist to detect the cases that may have been missed by phenotypic tests and enhance the NTM diagnosis capability to improve effective patient management.
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Affiliation(s)
- Ellappan Kalaiarasan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Kalpana Thangavelu
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Krishnakumariamma Krishnapriya
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Muthaiah Muthuraj
- Intermediate Reference Laboratory, Government Hospital for Chest Diseases, Pondicherry, India
| | - Maria Jose
- Intermediate Reference Laboratory, Government Hospital for Chest Diseases, Pondicherry, India
| | - Noyal Mariya Joseph
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India.
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Thumamo Pokam BD, Yeboah-Manu D, Teyim PM, Guemdjom PW, Wabo B, Fankep ABD, Okonu RE, Asuquo AE. A pilot study on the genetic diversity of Mycobacterium tuberculosis complex strains from tuberculosis patients in the Littoral region of Cameroon. J Clin Tuberc Other Mycobact Dis 2020; 21:100182. [PMID: 32964145 PMCID: PMC7490731 DOI: 10.1016/j.jctube.2020.100182] [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] [Indexed: 12/02/2022] Open
Abstract
The Xpert MTB/RIF provides a rapid MDR detection and management of TB patients. The Cameroon family is the predominant genotype in the Littoral region of Cameroon. The UgandaI sublineage is likely associated with RIF resistance in the study area. The mapping of the UgandaI sublineage is essential for MDR control in the country.
Background The re-emergence of tuberculosis (TB) worldwide, compounded by multi-drug resistance (MDR) of the causative agents constitutes a major challenge to the management of the disease. Rapid diagnosis and accurate strain identification are pivotal to the control of the disease. This pilot study investigated the genetic diversity of Mycobacterium tuberculosis complex (MTBC) strains from TB patients in the Littoral region of Cameroon as well as their resistance to rifampicin (RIF). Patients and methods This was a cross sectional hospital-based study carried out between January and December 2017 and including 158 isolates from sputum smear positive individuals [105 (66.5%) males and 53 (33.5%) females]. Sputum samples were tested using Xpert MTB/RIF, followed by culture on Lowenstein–Jensen medium. Isolates were further subjected to molecular characterization using IS6110 typing, deletion analysis and spoligotyping. Results Thirteen (8.8%) of the 147 isolates with susceptibility results available were resistant to RIF. Drug resistance occurred in 5/50 (10%) female compared to 8/97 (8.2%) male (OR, 0.81; 0.25–2.62; p = 0.764), and there was no significant difference across the age ranges (p = 0.448). On the other hand, RIF resistance was associated (OR, 0.18, 95%CI, 0.05–0.69; p = 0.023) with previously treated patients [(4/14 (28.6%)] compared to new ones [9/133 (6.8%)]. The 150 identified lineages included among others 54 (36%) Cameroon, 18 (12%) UgandaI, 32 (21.3%) Haarlem, 17 (11.3%) Ghana, 9(6%) West African 1, 7(4.7%) Delhi/CAS, 4 (2.7%) LAM and 3 (2%) UgandaII. Of the 150 isolates, the major cluster was the Cameroon SIT 61, with 43(28.7%) isolates. Six (35.3%) of the 17 UgandaI sub-lineage were RIF resistant (OR, 9.58; 95%CI, 2.74–33.55, p = 0.001). Conclusion The cosmopolitan Littoral region presents with a wide Mycobacterium tuberculosis (MTB) strains diversity and the UgandaI sub-lineage likely associated with RIF resistance. Understanding the spread of this clade through surveillance will enhance TB control in the region.
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Affiliation(s)
- Benjamin D Thumamo Pokam
- Department of Medical Laboratory Science, University of Buea, Cameroon.,Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - D Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - P M Teyim
- Douala Tuberculosis Reference Laboratory, Littoral Region, Cameroon
| | - P W Guemdjom
- Department of Public Health, University of Buea, Cameroon
| | - B Wabo
- Department of Medical Laboratory Science, University of Buea, Cameroon
| | - A B D Fankep
- Department of Medical Laboratory Science, University of Buea, Cameroon
| | - R E Okonu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Anne E Asuquo
- Department of Medical Laboratory Science, College of Medicine, University of Calabar, Calabar, Nigeria
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A novel approach for tuberculosis diagnosis using exosomal DNA and droplet digital PCR. Clin Microbiol Infect 2020; 26:942.e1-942.e5. [DOI: 10.1016/j.cmi.2019.11.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 12/14/2022]
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15
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Development and Evaluation of a Single Dye Duplex Droplet Digital PCR Assay for the Rapid Detection and Quantification of Mycobacterium tuberculosis. Microorganisms 2020; 8:microorganisms8050701. [PMID: 32397601 PMCID: PMC7284639 DOI: 10.3390/microorganisms8050701] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 12/29/2022] Open
Abstract
Droplet digital PCR (ddPCR) is a third generation of PCR that was recently developed to overcome the challenges of real-time fluorescence-based quantitative PCR (qPCR) in absolute quantification of pathogens. Few studies have been done on tuberculosis (TB) detection and quantification using ddPCR despite its many advantages over qPCR. From the few studies, none explores a single dye duplex assay for the detection and quantification of TB. In this study, steps toward developing and evaluating a duplex single dye (FAM) assay for detecting two targets (IS6110 and IS1081) are clearly described using simplex and duplex experiments. To achieve this, various parameters are investigated, including annealing temperature, primer and probe concentration, sensitivity and specificity, sample concentration, and inter/intra-assay variability. From the results, primer and probe concentration, annealing temperature, and sample concentration have an effect on the position and separation of droplets in both simplex and duplex assays. The copies of target genes in a duplex assay can be estimated accurately using the threshold tool with little inter-assay (CV <1%) and intra-assay (CV <6%) variability when compared to simplex assays. The ddPCR assay specificity and sensitivity are both 100% when compared to qPCR. This work shows steps toward the detection and quantification of two targets in a single channel, enabling higher multiplexing to include more targets in future works.
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16
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Wu X, Tan G, Gao R, Yao L, Bi D, Guo Y, Yu F, Fan L. Assessment of the Xpert MTB/RIF Ultra assay on rapid diagnosis of extrapulmonary tuberculosis. Int J Infect Dis 2019; 81:91-96. [PMID: 30738907 DOI: 10.1016/j.ijid.2019.01.050] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/27/2019] [Accepted: 01/31/2019] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To evaluate the diagnostic performance of Xpert MTB/RIF Ultra for EPTB (Extrapulmonary Tuberculosis) patients on different types of extrapulmonary specimens from different anatomic sites. METHODS Patients with suspected EPTB were prospectively included, extrapulmonary specimens were collected and subjected to culture, Xpert and Xpert Ultra assays in accordance with relevant guidelines. RESULTS A total of 225 cases were included which contained 200 EPTB cases (43 culture-positive EPTB, 157 culture-negative EPTB which were diagnosed based on pathological results and a satisfied response to anti-TB treatment) and 25 non-EPTB cases. Sensitivities of Xpert Ultra and Xpert for culture-positive cases were 83.7% (95%CI, 68.7-92.7) and 67.4% (95% CI, 51.3-80.5) respectively. Specificities of Xpert Ultra and Xpert were 92.0% (95% CI, 72.5-98.6) and 96.0% (95% CI, 77.7-99.8) respectively. The sensitivities of Xpert Ultra, Xpert and culture for 200 EPTB cases were 52.5% (105/200, 95% CI, 45.4-59.6), 34.0% (68/200, 95% CI, 27.6-41.1) and 21.5% (43/200, 95% CI, 16.2-28.0) respectively. By comparison among different types of specimens, Xpert Ultra can detect 78.9% (56/71) of EPTB on fine-needle aspiration (FNA) tissues which was higher than that on pleural fluid (43.7% (45/103), p<0.05. CONCLUSIONS Xpert Ultra assay had a higher sensitivity than those of Xpert and culture on extrapulmonary specimens, which could be a promising approach for rapid EPTB diagnosis.
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Affiliation(s)
- Xiaocui Wu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Guangkun Tan
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Rongliang Gao
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lan Yao
- Clinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Dexi Bi
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Yinjuan Guo
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lin Fan
- Clinic and Research Center of Tuberculosis, Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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Abstract
This chapter focuses on the synthesis, functionalization, and applications of metallic, semiconductor, magnetic, and multifunctional nanoparticles. Synthesis methods such as chemical reduction, coprecipitation, seeding, microemulsion, hydrothermal synthesis, and sonoelectrodeposition are outlined. Functionalized nanoparticles are suitable for numerous applications. Several applications of nanoparticles in life sciences and the enviromment are discussed. Finally, some future trends are pointed out.
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Affiliation(s)
- Nguyen Hoang Nam
- Faculty of Physics, Hanoi University of Science, Vietnam National University, Hanoi, Hanoi, Vietnam,Nano and Energy Center, Hanoi University of Science, Vietnam National University, Hanoi, Hanoi, Vietnam
| | - Nguyen Hoang Luong
- Nano and Energy Center, Hanoi University of Science, Vietnam National University, Hanoi, Hanoi, Vietnam
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18
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Neshani A, Kamali Kakhki R, Sankian M, Zare H, Hooshyar Chichaklu A, Sayyadi M, Ghazvini K. Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example. BMC Infect Dis 2018; 18:517. [PMID: 30314460 PMCID: PMC6186143 DOI: 10.1186/s12879-018-3417-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we aimed to explain this method with the example of Mycobacterium tuberculosis complex and investigate its efficacy in a diagnostic test. METHODS A specific target was identified using modified genome comparison method and an in-house PCR test was designed. To determine the analytical sensitivity and specificity, 10 standard specimens were used. Also, 230 specimens were used to determine the clinical sensitivity and specificity. RESULTS The identity and query cover of our new diagnostic target (5KST) were ≥ 90% with M. tuberculosis complex. The 5KST-PCR sensitivity was 100% for smear-positive, culture-positive and 85.7% for smear-negative, culture-positive specimens. All of 100 smear-negative, culture-negative specimens were negative in 5KST-PCR (100% clinical specificity). Analytical sensitivity of 5KST-PCR was approximately 1 copy of genomic DNA per microliter. CONCLUSIONS Modified genome comparison method is a confident way to find specific targets for use in diagnostic tests. Accordingly, the 5KST-PCR designed in this study has high sensitivity and specificity and can be replaced for conventional TB PCR tests.
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Affiliation(s)
- Alireza Neshani
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Kamali Kakhki
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojtaba Sankian
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hosna Zare
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Hooshyar Chichaklu
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Sayyadi
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
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Evaluation of the Xpert MTB/RIF Ultra Assay for Direct Detection of Mycobacterium tuberculosis Complex in Smear-Negative Extrapulmonary Samples. J Clin Microbiol 2018; 56:JCM.00659-18. [PMID: 29950333 DOI: 10.1128/jcm.00659-18] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023] Open
Abstract
The rapid detection of Mycobacterium tuberculosis complex (MTUBC) in clinical samples is essential for successful treatment. New techniques such as real-time PCR have been developed in order to facilitate rapid diagnosis, but their sensitivity is low in extrapulmonary specimens, due to the low bacillary load in such samples. A next-generation assay has recently been developed to try to overcome this limitation. The aim of this study was to analyze the effectiveness of the Xpert MTB/RIF Ultra (GX-Ultra) for the detection of MTUBC DNA in 108 smear-negative extrapulmonary specimens that were MTUBC culture positive. In addition, 40 extrapulmonary culture-negative samples and 20 samples with nontuberculous mycobacteria were tested to evaluate the specificity of the assay. All samples were collected between May 1999 and May 2017. The GX-Ultra detected DNA of MTUBC in 82 extrapulmonary specimens that were MTUBC culture positive (75.9% sensitivity; 95% confidence interval [CI], 66.6 to 83.4%). The assay was negative for all clinical specimens that were MTUBC culture negative and the samples with nontuberculous mycobacteria (100% specificity). Furthermore, two (1.8%) samples presented mutations related to rifampin resistance. The highest sensitivity was obtained in samples of lymph nodes (94.1%) and nonsterile fluids (93.7%), followed by tissue specimens (86.6%), stool material (80%), abscess aspirates (64.7%), and sterile fluids (60.5%). Pleural fluids, one of the least optimal samples for detecting DNA of MTUBC, were GX-Ultra positive in 10/21 (47.6%) of cases. In summary, GX-Ultra showed excellent specificity and high sensitivity in paubacillary specimens, making it a useful tool for rapid diagnosis of extrapulmonary tuberculosis.
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Amlerova J, Bitar I, Hrabak J. Genotyping of Mycobacterium tuberculosis using whole genome sequencing. Folia Microbiol (Praha) 2018; 63:537-545. [PMID: 29550921 DOI: 10.1007/s12223-018-0599-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 03/08/2018] [Indexed: 11/26/2022]
Abstract
Tuberculosis (TB) is considered one of the most serious infectious diseases worldwide. Effective control of tuberculosis infection involves multiple steps, such as reliable detection, treatment, an epidemiological control as a part of case management, and further surveillance and monitoring of TB spread in the human population. Due to the accelerating advances in molecular biology, especially in DNA sequencing, in the past decade, the application of these methods has become crucial for TB evolution studies, differentiation of Mycobacterium tuberculosis genotypes, and their distribution. Currently, several molecular genetic methods are available. The oldest typing methods (e.g., IS6110-RFLP, spoligotyping, and MIRU-VNTR) can discover the chain of transmission to the patient. Currently, whole genome sequencing facilitates is furthermore able to identify the source of infection, the transmission trays among individuals sharing the same isolate, as well as determination of the TB evolution and its resistance to antituberculotic agents. It is obvious that this technique will become a new gold standard in genotyping methods in tuberculosis molecular epidemiological studies. In this article, molecular genetic typing methods with a special focus on whole genome sequencing and data management are reviewed.
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Affiliation(s)
- Jana Amlerova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Alej Svobody 80, 304 60, Pilsen, Czech Republic.
| | - Ibrahim Bitar
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Jaroslav Hrabak
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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Evaluation of Loopamp™MTBC detection kit for diagnosis of pulmonary tuberculosis at a peripheral laboratory in a high burden setting. Diagn Microbiol Infect Dis 2017; 90:190-195. [PMID: 29246776 DOI: 10.1016/j.diagmicrobio.2017.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 11/22/2022]
Abstract
The Loopamp™MTBC detection kit (TB-LAMP) was designed to replace the sputum smear microscopy for the diagnosis of pulmonary tuberculosis. We evaluated its performance at a peripheral laboratory in Vietnam. The sensitivity of TB-LAMP was 45.5% (28.1%-63.6%), which was equal to 3-sputum smear microscopy but lower than that of Xpert MTB/RIF (87.8% [71.8%-96.6%]). In patients with culture-confirmed TB, sensitivity was 80% (51.9%-95.7%) in smear-positive and 16.7% (3.5%-41.4%) in smear-negative cases. The specificity of TB-LAMP was 95.1% (92.7%-96.9%), which was lower than that of smear microscopy (98.9% [97.5%-99.7%]) and Xpert MTB/RIF (99.3% [98.1%-99.9%]) (P<0.05). The probability of TB detection by TB-LAMP was more influenced by sample quality and viscosity than were smear microscopy, Xpert MTB/RIF, and culture. The present data do not support the use of TB-LAMP as a replacement test for smear microscopy in peripheral laboratories.
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Tyagi S, Sharma N, Tyagi JS, Haldar S. Challenges in pleural tuberculosis diagnosis: existing reference standards and nucleic acid tests. Future Microbiol 2017; 12:1201-1218. [PMID: 28972418 DOI: 10.2217/fmb-2017-0028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pleural tuberculosis (pTB) is a grave form of extrapulmonary tuberculosis. Microbiological tests are usually found to be inadequate for pTB diagnosis. The absence of a uniform 'composite reference standard' is challenging; therefore, diagnosis is usually performed using a combination of diversified criteria. Nucleic acid tests vary in diagnostic accuracy and have not yet been integrated into clinical decision making. This review assesses the varied criteria used for pTB classification and the challenges afflicting pleural fluid-based DNA diagnostic tests, namely, PCR and Xpert® MTB/RIF. In the 58 studies (PCR: n = 33; Xpert: n = 25) analyzed, reference standards were heterogeneous and PCR/Xpert pooled sensitivity values (range: 0-100%) were inadequate. However, the consistent high specificity of Xpert (range: 90-100%) indicated its utility as a 'rule-in' test. There is an urgent need to evaluate existing and new molecular tests in well-designed studies to accurately assess their utility for pTB diagnosis. To conclude, rapid and accurate tests are warranted for pTB diagnosis.
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Affiliation(s)
- Shaifali Tyagi
- Center for Bio-design & Diagnostics, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box No 04, Faridabad 121001, India
| | - Neera Sharma
- Department of Biochemistry, Dr RML Hospital, New Delhi 110001, India
| | - Jaya Sivaswami Tyagi
- Center for Bio-design & Diagnostics, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box No 04, Faridabad 121001, India.,Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sagarika Haldar
- Center for Bio-design & Diagnostics, Translational Health Science & Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO Box No 04, Faridabad 121001, India
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Kanniappan P, Ahmed SA, Rajasekaram G, Marimuthu C, Ch'ng ES, Lee LP, Raabe CA, Rozhdestvensky TS, Tang TH. RNomic identification and evaluation of npcTB_6715, a non-protein-coding RNA gene as a potential biomarker for the detection of Mycobacterium tuberculosis. J Cell Mol Med 2017; 21:2276-2283. [PMID: 28756649 PMCID: PMC5618688 DOI: 10.1111/jcmm.13148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/01/2017] [Indexed: 01/15/2023] Open
Abstract
Technological advances in RNA biology greatly improved transcriptome profiling during the last two decades. Besides the discovery of many small RNAs (sRNA) that are involved in the physiological and pathophysiological regulation of various cellular circuits, it becomes evident that the corresponding RNA genes might also serve as potential biomarkers to monitor the progression of disease and treatment. sRNA gene candidate npcTB_6715 was previously identified via experimental RNomic (unpublished data), and we report its application as potential biomarker for the detection of Mycobacterium tuberculosis (MTB) in patient samples. For proof of principle, we developed a multiplex PCR assay and report its validation with 500 clinical cultures, positive for Mycobacteria. The analysis revealed 98.9% sensitivity, 96.1% specificity, positive and negative predictive values of 98.6% and 96.8%, respectively. These results underscore the diagnostic value of the sRNA gene as diagnostic marker for the specific detection of MTB in clinical samples. Its successful application and the general ease of PCR‐based detection compared to standard bacterial culture techniques might be the first step towards ‘point‐of‐care’ diagnostics of Mycobacteria. To the best of our knowledge, this is the first time for the design of diagnostic applications based on sRNA genes, in Mycobacteria.
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Affiliation(s)
- Priyatharisni Kanniappan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, Penang, Malaysia.,Department of Pathology, Johor Bahru General Hospital, Johor, Malaysia
| | - Siti Aminah Ahmed
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, Penang, Malaysia
| | | | - Citartan Marimuthu
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, Penang, Malaysia
| | - Ewe Seng Ch'ng
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, Penang, Malaysia
| | - Li Pin Lee
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, Penang, Malaysia
| | - Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), University of Muenster, Münster, Germany.,Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB), Neuruppin, Germany.,Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation (ZMBE), University of Muenster, Münster, Germany
| | | | - Thean Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Kepala Batas, Penang, Malaysia
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Khosravi AD, Alami A, Meghdadi H, Hosseini AA. Identification of Mycobacterium tuberculosis in Clinical Specimens of Patients Suspected of Having Extrapulmonary Tuberculosis by Application of Nested PCR on Five Different Genes. Front Cell Infect Microbiol 2017; 7:3. [PMID: 28144587 PMCID: PMC5239771 DOI: 10.3389/fcimb.2017.00003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/03/2017] [Indexed: 01/05/2023] Open
Abstract
Definitive and rapid diagnosis of extrapulmonary tuberculosis (EPTB) is challenging since conventional techniques have limitations due to the paucibacillary nature of the disease. To increase the sensitivity of detection of Mycobacterium tuberculosis (MTB) in EPTB specimens, we performed a nested PCR assay targeting several genes of MTB on EPTB specimens. A total of 100 clinical specimens from suspected cases of EPTB were processed. Standard staining for acid fast bacilli (AFB) was performed as the preliminary screening test. Extracted DNAs from specimens were subjected to Nested PCR technique for the detection of five different MTB target genes of IS6110, IS1081, hsp65kd, mbp64, and mtp40. On performing AFB staining, only 13% of specimens were positive, of which ascites fluid (33.3%), followed by pleural effusion (30.8%) showed the greatest AFB positivity rate. We demonstrated slight improvement in yields in lymph node which comprised the majority of specimens in this study, by employing PCR targeted to IS6110- and hsp65-genes in comparison to AFB staining. However, the yields in ascites fluid and pleural effusion were not substantially improved by PCR, but those from bone and wound were, as in nested PCR employing either gene, the same positivity rate were obtained for ascites fluid (33.3%), while for pleural effusion specimens only IS1081 based PCR showed identical positivity rate with AFB stain (30.8%). The results for bone and wound specimens, however, demonstrated an improved yield mainly by employing IS1081 gene. Here, we report higher detection rate of EPTB in clinical specimens using five different targeted MTB genes. This nested PCR approach facilitates the comparison and the selection of the most frequently detected genes. Of course this study demonstrated the priority of IS1081 followed by mtp40 and IS6110, among the five tested genes and indicates the effectiveness of any of the three genes in the design of an efficient nested-PCR test that facilitates an early diagnosis of paucibacillary EPTB cases, which are difficult to diagnose with the available standard.
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Affiliation(s)
- Azar D Khosravi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran; Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
| | - Ameneh Alami
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences Ahvaz, Iran
| | - Hossein Meghdadi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences Ahvaz, Iran
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Typing Method for the QUB11a Locus of Mycobacterium tuberculosis: IS 6110 Insertions and Tandem Repeat Analysis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5216530. [PMID: 27812529 PMCID: PMC5080463 DOI: 10.1155/2016/5216530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/22/2016] [Indexed: 11/17/2022]
Abstract
QUB11a is used as a locus for variable number of tandem repeats (VNTR) analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp) that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and BsmBI digestion. All 29 large QUB11a fragments (>1,200 bp) investigated contained IS6110 insertions and varied in the number of repeats (18 patterns) and location of IS6110 insertions. This method allows VNTR analysis with high discrimination.
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Kyselicová K, Šebest L, Bognár C, Šarkan M, Baldovič M, Beňuš R, Kádaši Ľ. Molecular detection of Mycobacterium tuberculosis complex in the 8th century skeletal remains from the territory of Slovakia. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Raj A, Singh N, Gupta KB, Chaudhary D, Yadav A, Chaudhary A, Agarwal K, Varma-Basil M, Prasad R, Khuller GK, Mehta PK. Comparative Evaluation of Several Gene Targets for Designing a Multiplex-PCR for an Early Diagnosis of Extrapulmonary Tuberculosis. Yonsei Med J 2016; 57:88-96. [PMID: 26632387 PMCID: PMC4696977 DOI: 10.3349/ymj.2016.57.1.88] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/21/2015] [Accepted: 05/02/2015] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Diagnosis of extrapulmonary tuberculosis (EPTB) poses serious challenges. A careful selection of appropriate gene targets is essential for designing a multiplex-polymerase chain reaction (M-PCR) assay. MATERIALS AND METHODS We compared several gene targets of Mycobacterium tuberculosis, including IS6110, devR, and genes encoding MPB-64 (mpb64), 38kDa (pstS1), 65kDa (hsp65), 30kDa (fbpB), ESAT-6 (esat6), and CFP-10 (cfp10) proteins, using PCR assays on 105 EPTB specimens. From these data, we chose the two best gene targets to design an M-PCR. RESULTS Among all gene targets tested, mpb64 showed the highest sensitivity (84% in confirmed cases and 77.5% in clinically suspected cases), followed by IS6110, hsp65, 38kDa, 30kDa, esat6, cfp10, and devR. We used mpb64+IS6110 for designing an M-PCR assay. Our M-PCR assay demonstrated a high sensitivity of 96% in confirmed EPTB cases and 88.75% in clinically suspected EPTB cases with a high specificity of 100%, taking clinical diagnosis as the gold standard. CONCLUSION These M-PCR results along with the clinical findings may facilitate an early diagnosis of EPTB patients and clinical management of disease.
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Affiliation(s)
- Ankush Raj
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Netrapal Singh
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India
| | - Krishna B Gupta
- Department of TB & Respiratory Medicine, Postgraduate Institute of Medical Sciences (PGIMS), Rohtak, India
| | - Dhruva Chaudhary
- Department of Pulmonary and Critical Care Medicine, Postgraduate Institute of Medical Sciences (PGIMS), Rohtak, India
| | - Aparna Yadav
- Department of Microbiology, Postgraduate Institute of Medical Sciences (PGIMS), Rohtak, India
| | - Anil Chaudhary
- Rajan Babu Institute of Pulmonary Medicine and Tuberculosis (RBIPMT), Delhi, India
| | - Kshitij Agarwal
- Rajan Babu Institute of Pulmonary Medicine and Tuberculosis (RBIPMT), Delhi, India
| | | | - Rajendra Prasad
- Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Gopal K Khuller
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Promod K Mehta
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, India.
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Sanjuan-Jimenez R, Toro-Peinado I, Bermudez P, Colmenero JD, Morata P. Comparative Study of a Real-Time PCR Assay Targeting senX3-regX3 versus Other Molecular Strategies Commonly Used in the Diagnosis of Tuberculosis. PLoS One 2015; 10:e0143025. [PMID: 26600434 PMCID: PMC4658205 DOI: 10.1371/journal.pone.0143025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
Background Nucleic acid amplification tests are increasingly used for the rapid diagnosis of tuberculosis. We undertook a comparative study of the efficiency and diagnostic yield of a real-time PCR senX3-regX3 based assay versus the classical IS6110 target and the new commercial methods. Methods This single-blind prospective comparative study included 145 consecutive samples: 76 from patients with culture-confirmed tuberculosis (86.8% pulmonary and 13.2% extrapulmonary tuberculosis: 48.7% smear-positive and 51.3% smear-negative) and 69 control samples (24 from patients diagnosed with non-tuberculous mycobacteria infections and 45 from patients with suspected tuberculosis which was eventually ruled out). All samples were tested by two CE-marked assays (Xpert®MTB/RIF and AnyplexTM plus MTB/NTM) and two in-house assays targeting senX3-regX3 and the IS6110 gene. Results The detection limit ranged from 1.00E+01 fg for Anyplex, senX3-regX3 and IS6110 to 1.00E+04 fg for Xpert. All three Xpert, senX3-regX3 and IS6110 assays detected all 37 smear-positive cases. Conversely, Anyplex was positive in 34 (91.9%) smear-positive cases. In patients with smear-negative tuberculosis, differences were observed between the assays; Xpert detected 22 (56.41%) of the 39 smear-negative samples, Anyplex 24 (61.53%), senX3-regX3 28 (71.79%) and IS6110 35 (89.74%). Xpert and senX3-regX3 were negative in all control samples; however, the false positive rate was 8.7% and 13% for Anyplex and IS6110, respectively. The overall sensitivity was 77.6%, 85.7%, 77.3% and 94.7% and the specificity was 100%, 100%, 90.8% and 87.0% for the Xpert, senX3-regX3, Anyplex and IS6110 assays, respectively. Conclusion Real-time PCR assays targeting IS6110 lack the desired specificity. The Xpert MTB/RIF and in-house senX3-regX3 assays are both sensitive and specific for the detection of MTBC in both pulmonary and extrapulmonary samples. Therefore, the real time PCR senX3-regX3 based assay could be a useful and complementary tool in the diagnosis of tuberculosis.
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Affiliation(s)
- Rocio Sanjuan-Jimenez
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
- * E-mail:
| | | | - Pilar Bermudez
- Microbiology Service, Regional University Hospital, Malaga, Spain
| | - Juan D. Colmenero
- Infectious Diseases Service, Regional University Hospital, Malaga, Spain
| | - Pilar Morata
- Biochemistry, Molecular Biology and Immunology Department, Faculty of Medicine, University of Malaga, Malaga, Spain
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Lewandowsky's Rosaceiform Eruption: a Form of Cutaneous Tuberculosis Confirmed by PCR in Two Patients. Dermatol Ther (Heidelb) 2014; 5:67-76. [PMID: 25518812 PMCID: PMC4374068 DOI: 10.1007/s13555-014-0066-x] [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: 05/26/2014] [Indexed: 12/02/2022] Open
Abstract
Introduction Cutaneous tuberculosis (TBC) is a chronic disease caused by Mycobacterium tuberculosis, and is present in less than 1–2% of all TBC cases. The current problem with diagnosis is the demonstration of bacillus in the skin, especially paucibacillar forms, where sources like polymerase chain reaction (PCR) have improved diagnostic capacity. Case Presentation Two cases of cutaneous TBC are reported. The first patient was 52-year-old woman with facial erythematous papulo-nodular lesions which had been developing for 4 months, and had previously been treated as acne rosacea, with partial response. Histopathological studies showed chronic granulomatous inflammation. TBC was suspected, so PCR was performed, which showed positive for M. tuberculosis. The second case was a 43-year-old woman with a facial rosaceiform plaque which began 6 months previously, and was treated as rosacea without any change for 5 months. Skin biopsy and PCR were positive for TBC. Both cases were treated using primary schedule for TBC, and both presented a favorable response. Discussion A clinical profile called Lewandowsky’s rosacea-like eruption has been previously described. The condition has been questioned for years and was later removed from the spectrum of tuberculids and cutaneous TBC for not being able to isolate microorganisms in skin samples, a situation that might now change. In paucibacillar forms, when culture and staining are negative and TBC is still suspected, it is recommended to use DNA amplification by PCR for an accurate diagnosis. Both cases bring up the concern about once again bringing Lewandowsky’s rosaceiform eruption into the spectrum of cutaneous TBC, and the discussion about the current definition of tuberculid. Electronic supplementary material The online version of this article (doi:10.1007/s13555-014-0066-x) contains supplementary material, which is available to authorized users.
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Evaluation of hsp65 nested PCR-restriction analysis (PRA) for diagnosing tuberculosis in a high burden country. BIOMED RESEARCH INTERNATIONAL 2013; 2013:391549. [PMID: 24260739 PMCID: PMC3821893 DOI: 10.1155/2013/391549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/08/2013] [Indexed: 11/17/2022]
Abstract
Current study evaluated the hsp65 Nested PCR Restriction Fragment Length Polymorphism Analysis (hsp65 Nested PCR-PRA) to detect and
identify Mycobacterium tuberculosis complex directly in clinical samples for a rapid and specific diagnosis of tuberculosis (TB). hsp65 Nested PCR-PRA was
applied directly to 218 clinical samples obtained from 127 patients suspected of TB or another mycobacterial infection from July 2009 to July 2010. The hsp65 Nested
PCR-PRA showed 100% sensitivity and 95.0 and 93.1% specificity in comparison with culture and microscopy (acid fast bacillus smear), respectively. hsp65 Nested
PCR-PRA was shown to be a fast and reliable assay for diagnosing TB, which may contribute towards a fast diagnosis that could help the selection of appropriate chemotherapeutic and early
epidemiological management of the cases which are of paramount importance in a high TB burden country.
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