Amplification-Free DNA Detection Using a Microtip-Sensor Decorated With LNA Probes for Rapid TB Screening

2011 ◽  
Author(s):  
Shinnosuke Inoue ◽  
Woon-Hong Yeo ◽  
Jong-Hoon Kim ◽  
Jae-Hyun Chung ◽  
Kyong-Hoon Lee ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Staphylococcus Epidermidis ◽  
Genomic Dna ◽  
Bacterial Culture ◽  
Low Cost ◽  
Surrogate Marker ◽  
High Sensitivity ◽  
Diagnostic Methods ◽  
Nucleic Acid Amplification ◽  
Highly Sensitive

Tuberculosis (TB) is an epidemic affecting one-third of the world’s population, mostly in developing and low-resource settings. People having active pulmonary TB are considered highly infectious; therefore, it is critical to identify and treat these patients rapidly before spreading to others. However, the most reliable TB diagnostic methods of bacterial culture or nucleic acid amplification are time-consuming and expensive. The challenge of TB diagnosis lies in highly sensitive and specific screening with low cost. Here, we present an LNA-modified microtip-sensor, which is capable of selectively detecting low-abundance DNA from bacteria. When genomic DNA of Bacillus Calmette-Gue´rin (BCG, a surrogate marker of Mycobacterium bovis), and genomic DNA of Staphylococcus epidermidis (S. epi) are used, the microtip-sensor yields the detection limit of 1,000 copies/mL within 20 minutes. The high sensitivity and specificity approaching nucleic acid amplification methods can potentially overcome the current challenges for rapid TB screening.

scholarly journals Diagnostic performance of nucleic acid tests in tuberculous pleurisy

2020 ◽  
Author(s):  
Min Han ◽  
He-ping Xiao ◽  
Liping Yan
Keyword(s):  
Nucleic Acid ◽  
Pleural Effusion ◽  
Low Cost ◽  
Extrapulmonary Tuberculosis ◽  
Diagnostic Methods ◽  
Nucleic Acid Amplification ◽  
First Choice ◽  
Area Under Roc Curve ◽  
Tuberculous Pleurisy ◽  
Culture Positive

Abstract Background: Tuberculous pleurisy (TBP) is the most common form of extrapulmonary tuberculosis (TB). However, rapid diagnostic methods with high accuracy for tuberculous pleurisy are urgently needed. In the present study, we evaluated the diagnostic accuracy of Xpert MTB/RIF, LAMP and SAT-TB assay with pleural fluids from from culture-positive TBP patients. Methods: We prospectively enrolled 300 patients with exudative pleural effusions used as the samples for Xpert MTB/RIF, LAMP and SAT-TB assay. Of these, 265 including 223 patients diagnosed with TP and 42 non-TB patients used as controls were analyzed. Results: The sensitivities of Xpert MTB/RIF (27.4%) , LAMP (26.5%) and SAT-TB assay (32.3%) were significantly higher than that of pleural effusion smear (14.3% , X 2 = 20.65, P < 0.001), whereas they were much lower than expected for the analysis of pleural effusion samples. Both SAT-TB assay and Xpert MTB/RIF demonstrated high specificities (100%) and PPVs (100%), but the NPVs of all of the tests were < 22%. The area under ROC curve of pleural effusionsmear, LAMP, Xpert MTB/RIF and SAT-TB assays was 0.524 (95% CI 0.431–0.617), 0.632 (95% CI 0.553–0.71), 0.637 (95% CI 0.56–0.714) and 0.673 (95% CI 0.6–0.745). SAT-TB assays had the highest AUC. Conclusion: Nucleic acid amplification tests are not the first choice in the diagnosis of tuberculous pleurisy. In this type of test, SAT-TB is recommended because of its low cost, relatively more accurate compared with the other two tests. This prospective study was approved by The Ethics Committee of the Shanghai Pulmonary Hospital (approval number: K19-148). ClinicalTrials.gov identifier: ChiCTR1900026234. Key words : Xpert MTB/RIF; AmpSure simultaneous amplification and testing; loop-mediated isothermal amplification; diagnosis; tuberculosis

scholarly journals Diagnostic performance of nucleic acid tests in tuberculous pleurisy

2020 ◽  
Author(s):  
Min Han ◽  
He-ping Xiao ◽  
Liping Yan
Keyword(s):  
Nucleic Acid ◽  
Pleural Effusion ◽  
Low Cost ◽  
Extrapulmonary Tuberculosis ◽  
Diagnostic Methods ◽  
Nucleic Acid Amplification ◽  
First Choice ◽  
Area Under Roc Curve ◽  
Tuberculous Pleurisy ◽  
Culture Positive

Abstract Background: Tuberculous pleurisy (TBP) is the most common form of extrapulmonary tuberculosis (TB). However, rapid diagnostic methods with high accuracy for tuberculous pleurisy are urgently needed. In the present study, we evaluated the diagnostic accuracy of Xpert MTB/RIF, LAMP and SAT-TB assay with pleural fluids from from culture-positive TBP patients. Methods: We prospectively enrolled 300 patients with exudative pleural effusions used as the samples for Xpert MTB/RIF, LAMP and SAT-TB assay. Of these, 265 including 223 patients diagnosed with TP and 42 non-TB patients used as controls were analyzed. Results: The sensitivities of Xpert MTB/RIF (27.4%) , LAMP (26.5%) and SAT-TB assay (32.3%) were significantly higher than that of pleural effusion smear (14.3% , X 2 = 20.65, P < 0.001), whereas they were much lower than expected for the analysis of pleural effusion samples. Both SAT-TB assay and Xpert MTB/RIF demonstrated high specificities (100%) and PPVs (100%), but the NPVs of all of the tests were < 22%. The area under ROC curve of pleural effusionsmear, LAMP, Xpert MTB/RIF and SAT-TB assays was 0.524 (95% CI 0.431–0.617), 0.632 (95% CI 0.553–0.71), 0.637 (95% CI 0.56–0.714) and 0.673 (95% CI 0.6–0.745). SAT-TB assays had the highest AUC. Conclusion: Nucleic acid amplification tests are not the first choice in the diagnosis of tuberculous pleurisy. In this type of test, SAT-TB is recommended because of its low cost, relatively more accurate compared with the other two tests. This prospective study was approved by The Ethics Committee of the Shanghai Pulmonary Hospital (approval number: K19-148). ClinicalTrials.gov identifier: ChiCTR1900026234. Key words : Xpert MTB/RIF; AmpSure simultaneous amplification and testing; loop-mediated isothermal amplification; diagnosis; tuberculosis

scholarly journals Comparison of 3 Nucleic Acid Amplification Tests and a Rapid Antigen Test with Culture for the Detection of Group A Streptococci from Throat Swabs

2019 ◽  
Vol 4 (2) ◽  
pp. 164-169 ◽  
Author(s):  
Kyle G Parker ◽  
Sumanth Gandra ◽  
Scott Matushek ◽  
Kathleen G Beavis ◽  
Vera Tesic ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Predictive Value ◽  
Bacterial Culture ◽  
Group A Streptococcus ◽  
Point Of Care ◽  
High Sensitivity ◽  
Ease Of Use ◽  
Nucleic Acid Amplification ◽  
Gold Standard Method ◽  
Group A

Abstract Background Recently, the US Food and Drug Administration cleared 3 nucleic acid amplification test (NAAT) assays for detection of Streptococcus pyogenes [group A Streptococcus (GAS)] in pharyngeal specimens. However, there are limited studies evaluating the performance of these NAAT assays. Methods We compared the results of 3 NAATs (cobas Liat, Luminex Aries, and Cepheid Xpert Xpress) and a rapid antigen assay (Quidel QuickVue in-line strep A) with the accepted gold standard method, bacterial culture. Results Sixty-eight throat swab specimens collected between August and October 2017 were tested. Compared to bacterial culture, the sensitivities, specificities, positive predictive value, and negative predictive value for detecting GAS were as follows: cobas Liat: 100%, 97.4%, 96.7%, and 100%; Cepheid Xpert: 100%, 97.4%, 96.7%, and 100%; Luminex Aries: 95.2%, 100%, 100%, and 95.5%. The Quidel QuickVue in-line strep A assay showed poor sensitivity, detecting only 5.2% of culture-positive specimens. Conclusion The 3 NAATs have high sensitivity when compared with bacterial culture for detection of GAS. With rapid turnaround time and ease of use, these tests can be considered as reliable point-of-care tests for the diagnosis of GAS, replacing the need for back-up culture.

scholarly journals Diagnostic performance of nucleic acid tests in tuberculous pleurisy

2019 ◽  
Author(s):  
He-ping Xiao ◽  
Liping Yan ◽  
Min Han
Keyword(s):  
Nucleic Acid ◽  
Pleural Effusion ◽  
Low Cost ◽  
Extrapulmonary Tuberculosis ◽  
Diagnostic Methods ◽  
Nucleic Acid Amplification ◽  
First Choice ◽  
Area Under Roc Curve ◽  
Tuberculous Pleurisy ◽  
Culture Positive

Abstract Background: Tuberculous pleurisy (TBP) is the most common form of extrapulmonary tuberculosis (TB). However, rapid diagnostic methods with high accuracy for tuberculous pleurisy are urgently needed. In the present study, we evaluated the diagnostic accuracy of Xpert MTB/RIF, LAMP and SAT-TB assay with pleural fluids from from culture-positive TBP patients. Methods: We prospectively enrolled 300 patients with exudative pleural effusions used as the samples for Xpert MTB/RIF, LAMP and SAT-TB assay. Of these, 265 including 223 patients diagnosed with TP and 42 non-TB patients used as controls were analyzed. Results: The sensitivities of Xpert MTB/RIF (27.4%) , LAMP (26.5%) and SAT-TB assay (32.3%) were significantly higher than that of pleural effusion smear (14.3% , X2 = 20.65, P < 0.001), whereas they were much lower than expected for the analysis of pleural effusion samples. Both SAT-TB assay and Xpert MTB/RIF demonstrated high specificities (100%) and PPVs (100%), but the NPVs of all of the tests were < 22%. The area under ROC curve of pleural effusion smear, LAMP, Xpert MTB/RIF and SAT-TB assays was 0.524 (95% CI 0.431–0.617), 0.632 (95% CI 0.553–0.71), 0.637 (95% CI 0.56–0.714) and 0.673 (95% CI 0.6–0.745). SAT-TB assays had the highest AUC. Conclusion: Nucleic acid amplification tests are not the first choice in the diagnosis of tuberculous pleurisy. In this type of test, SAT-TB is recommended because of its low cost, relatively more accurate compared with the other two tests. This prospective study was approved by The Ethics Committee of the Shanghai Pulmonary Hospital (approval number: K19-148). ClinicalTrials.gov identifier: ChiCTR1900026234.

Highly sensitive detection of Cr(vi) in groundwater by bimetallic NiFe nanoparticles

2017 ◽  
Vol 9 (6) ◽  
pp. 1031-1037 ◽  
Author(s):  
Jingtao Liu ◽  
Yu Ding ◽  
Lifei Ji ◽  
Xin Zhang ◽  
Fengchun Yang ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Hexavalent Chromium ◽  
Low Cost ◽  
High Sensitivity ◽  
Sensitive Detection ◽  
Toxic Heavy Metal ◽  
Metal Pollutants ◽  
Highly Sensitive ◽  
Highly Sensitive Detection ◽  
Heavy Metal Pollutants

Hexavalent chromium (Cr(vi)) is one of the most toxic heavy metal pollutants in groundwater, and thus the detection of Cr(vi) with high sensitivity, accuracy, and simplicity and low cost is of great importance.

Highly sensitive, stable, and precise detection of dopamine with carbon dots/tyrosinase hybrid as fluorescent probe

RSC Advances ◽  
2014 ◽  
Vol 4 (87) ◽  
pp. 46437-46443 ◽  
Author(s):  
Hao Li ◽  
Juan Liu ◽  
Manman Yang ◽  
Weiqian Kong ◽  
Hui Huang ◽  
...  
Keyword(s):  
Fluorescent Probe ◽  
Carbon Dots ◽  
Low Cost ◽  
High Sensitivity ◽  
Highly Sensitive

The carbon dots/tyrosinase hybrid as a low-cost fluorescent probe for the detection of dopamine exhibits high sensitivity, stability, and precision.

scholarly journals Nucleic acid-based biosensors: analytical devices for prevention, diagnosis and treatment of diseases

Revista Vitae ◽  
2021 ◽  
Vol 28 (3) ◽  
Author(s):  
Laura Carvajal Barbosa ◽  
Diego Insuasty Cepeda ◽  
Andrés Felipe León Torres ◽  
Maria Mercedes Arias Cortes ◽  
Zuly Jenny Rivera Monroy ◽  
...  
Keyword(s):  
Food Safety ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Pathogenic Bacteria ◽  
High Selectivity ◽  
Low Cost ◽  
Analytical Techniques ◽  
High Sensitivity ◽  
Disease Status ◽  
Public Health Issue

BACKGROUND : Biosensing techniques have been the subject of exponentially increasing interest due to their performance advantages such as high selectivity and sensitivity, easy operation, low cost, short analysis time, simple sample preparation, and real-time detection. Biosensors have been developed by integrating the unique specificity of biological reactions and the high sensitivity of physical sensors. Therefore, there has been a broad scope of applications for biosensing techniques, and nowadays, they are ubiquitous in different areas of environmental, healthcare, and food safety. Biosensors have been used for environmental studies, detecting and quantifying pollutants in water, air, and soil. Biosensors also showed great potential for developing analytical tools with countless applications in diagnosing, preventing, and treating diseases, mainly by detecting biomarkers. Biosensors as a medical device can identify nucleic acids, proteins, peptides, metabolites, etc.; these analytes may be biomarkers associated with the disease status. Bacterial food contamination is considered a worldwide public health issue; biosensor-based analytical techniques can identify the presence or absence of pathogenic agents in food. OBJECTIVES: The present review aims to establish state-of-the-art, comprising the recent advances in the use of nucleic acid-based biosensors and their novel application for the detection of nucleic acids. Emphasis will be given to the performance characteristics, advantages, and challenges. Additionally, food safety applications of nucleic acid-based biosensors will be discussed. METHODS: Recent research articles related to nucleic acid-based biosensors, biosensors for detecting nucleic acids, biosensors and food safety, and biosensors in environmental monitoring were reviewed. Also, biosensing platforms associated with the clinical diagnosis and food industry were included. RESULTS: It is possible to appreciate that multiple applications of nucleic acid-based biosensors have been reported in the diagnosis, prevention, and treatment of diseases, as well as to identify foodborne pathogenic bacteria. The use of PNA and aptamers opens the possibility of developing new biometric tools with better analytical properties. CONCLUSIONS: Biosensors could be considered the most important tool for preventing, treating, and monitoring diseases that significantly impact human health. The aptamers have advantages as biorecognition elements due to the structural conformation, hybridization capacity, robustness, stability, and lower costs. It is necessary to implement biosensors in situ to identify analytes with high selectivity and lower detection limits.

scholarly journals Mass screening of asymptomatic persons for SARS-CoV-2 using saliva

2020 ◽  
Author(s):  
Isao Yokota ◽  
Peter Y Shane ◽  
Kazufumi Okada ◽  
Yoko Unoki ◽  
Yichi Yang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Mass Screening ◽  
Disease Outbreaks ◽  
High Sensitivity ◽  
Nucleic Acid Amplification ◽  
Contact Tracing ◽  
Global Pandemic ◽  
Screening Study ◽  
Highly Correlated ◽  
Few Data

Abstract Background COVID-19 has rapidly evolved to become a global pandemic due largely to the transmission of its causative virus through asymptomatic carriers. Detection of SARS-CoV-2 in asymptomatic people is an urgent priority for the prevention and containment of disease outbreaks in communities. However, few data are available in asymptomatic persons regarding the accuracy of PCR testing. Additionally, although self-collected saliva has significant logistical advantages in mass screening, its utility as an alternative specimen in asymptomatic persons is yet to be determined. Methods We conducted a mass-screening study to compare the utility of nucleic acid amplification, such as reverse transcriptase polymerase chain reaction (RT-PCR) testing, using nasopharyngeal swabs (NPS) and saliva samples from each individual in two cohorts of asymptomatic persons: the contact tracing cohort and the airport quarantine cohort. Results In this mass-screening study including 1,924 individuals, the sensitivity of nucleic acid amplification testing with nasopharyngeal and saliva specimens were 86% (90%CI:77-93%) and 92% (90%CI:83-97%), respectively, with specificities greater than 99.9%. The true concordance probability between the nasopharyngeal and saliva tests was estimated at 0.998 (90%CI:0.996-0.999) on the estimated airport prevalence at 0.3%. In positive individuals, viral load was highly correlated between NPS and saliva. Conclusion Both nasopharyngeal and saliva specimens had high sensitivity and specificity. Self-collected saliva is a valuable specimen to detect SARS-CoV-2 in mass screening of asymptomatic persons.

scholarly journals Highly Sensitive Non-Enzymatic Detection of Glucose at MWCNT-CuBTC Composite Electrode

2020 ◽  
Vol 10 (23) ◽  
pp. 8419
Author(s):  
Adriana Remes ◽  
Florica Manea ◽  
Sorina Motoc (m. Ilies) ◽  
Anamaria Baciu ◽  
Elisabeta I. Szerb ◽  
...  
Keyword(s):  
Composite Electrode ◽  
Glucose Sensor ◽  
Low Cost ◽  
Multiwall Carbon Nanotubes ◽  
Linear Sweep Voltammetry ◽  
High Sensitivity ◽  
Differential Pulse ◽  
Roll Mill ◽  
Highly Sensitive ◽  
Enzymatic Detection

A novel electrochemical glucose sensor was developed, based on a multiwall carbon nanotubes (MWCNTs)-copper-1,3,5-benzenetricarboxylic acid (CuBTC)-epoxy composite electrode, named MWCNT-CuBTC. The electrode nanocomposite was prepared by a two-roll mill procedure and characterized morphostructurally by scanning electron microscopy (SEM). The CuBTC formed defined crystals with a wide size distribution, which were well dispersed and embedded in the MWCNTs. Its electrical conductivity was determined by four-point probe contact (DC) conductivity measurements. The electroactive surface area, determined using cyclic voltammetry (CV), was found to be 6.9 times higher than the geometrical one. The results of the electrochemical measurements using CV, linear sweep voltammetry (LSV), differential pulse voltammetry (DPV), chronoamperometry (CA) and multiple pulse amperometry (MPA) showed that the MWCNT-CuBTC composite electrode displayed high electrocatalytic activity toward the oxidation of glucose and, as a consequence, very high sensitivity. The best sensitivity of 14,949 µAmM−1cm−1 was reached using MPA at the potential value of 0.6 V/SCE, which was much higher in comparison with other copper-based electrodes reported in the literature. The good analytical performance, low cost and simple preparation method make this novel electrode material promising for the development of an effective glucose sensor.

scholarly journals 1832. Development of an Ultrasensitive Field-Applicable Plasmodium falciparum Assay for Malaria Diagnosis and Eradication

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S42-S43
Author(s):  
Rose Lee ◽  
Helena De Puig Guixe ◽  
Jeffrey Dvorin ◽  
James Collins
Keyword(s):  
Plasmodium Falciparum ◽  
Nucleic Acid ◽  
Genomic Dna ◽  
Limit Of Detection ◽  
Malaria Diagnosis ◽  
High Sensitivity ◽  
Nucleic Acid Detection ◽  
One Pot ◽  
Minimal Sample ◽  
Isothermal Assay

Abstract Background Malaria control and eradication have been hampered by asymptomatic carriage which serves as a parasite reservoir. Low-density infections (< 100 parasites/microliter) frequently fall below the limit of detection (LOD) of microscopy and rapid diagnostic tests (RDT) which are antigen-based tests. Molecular methods such as polymerase chain reaction are capable of higher sensitivity yet remain impractical for resource-limited settings. We describe development of an isothermal assay using the nucleic acid detection platform SHERLOCK (Specific High-Sensitivity Enzymatic Reporter UnLOCKing), which may also be increasingly important as there has been rising detection of histidine-rich protein 2 (HRP2) gene deletions in Plasmodium spp. HRP2 is the most commonly used antigen in RDTs and deletion of this gene would render many RDTs obsolete. Methods SHERLOCK leverages the endonucleases of CRISPR-associated microbial adaptive immunity. Cas12a is an RNA-guided, DNA-cleaving enzyme, which can be programmed with guide RNAs to cleave nontarget reporter ssDNA. We exploit the nonspecific degradation of labeled ssDNA to detect the presence of the dsDNA target that activated Cas12a (Figure 1). Recombinase polymerase amplification (RPA) coupled with Cas12a detection enables a lower LOD. Plasmodium falciparum whole genomic DNA was compared with parasites cultured in red blood cells (RBCs) with known parasitemia and boiled at 95°C for 5 minutes for lysis of RBCs/parasites then diluted 1:2.5 to prevent solidification. Results This SHERLOCK assay detected simulated Plasmodium falciparum infection at attomolar LODs when applied to whole genomic DNA and simulated samples of infected RBCs spiked into whole blood. The genomic assay detected down to 0.2 parasites/microliter and the simulated sample detected to 10 parasites/microliter in the final reaction volume. In comparison, LODs from the initial input volume was 5aM and 250aM, respectively (Figure 2). Conclusion We demonstrate an isothermal nucleic acid detection platform capable of diagnosis in 60 minutes in a one-pot assay requiring minimal sample preparation and reaching an LOD recommended by the WHO for malaria eradication. In summary, we illustrate the utility of the SHERLOCK platform in application to malaria and global health. Disclosures All Authors: No reported Disclosures.

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