scholarly journals Evaluation of a rapid bacteriophage-based method for the detection of Mycobacterium tuberculosis in clinical samples

2003 ◽  
Vol 52 (4) ◽  
pp. 331-335 ◽  
Author(s):  
Ayman Mohamed Marei ◽  
Eman Mohamed El-Behedy ◽  
Heba Ali Mohtady ◽  
Afify Fahmy Afify
Keyword(s):  
Developing Countries ◽  
Mycobacterium Tuberculosis ◽  
Clinical Performance ◽  
Low Cost ◽  
Urine Samples ◽  
Clinical Samples ◽  
Pcr Assay ◽  
Microbiological Culture ◽  
Time To Diagnosis ◽  
Sensitivity Specificity

Rapid, sensitive and low-cost methods are needed urgently for the detection of Mycobacterium tuberculosis in clinical samples, especially in developing countries. To this end, the clinical performance of FASTPlaqueTBTM (a bacteriophage-based method) has been studied in parallel with microscopy, standard microbiological culture and in-house IS6110-based PCR methods. A total of 64 samples, including 42 sputum samples and 22 urine samples, were tested in this study. The sensitivity, specificity and overall accuracy values for the FASTPlaqueTB assay relative to that of culture were respectively 76.5, 95 and 90 %. The corresponding values for the in-house IS6110-based PCR assay were 88, 91 and 90 % and, for Ziehl–Neelsen staining, were 59, 95 and 85 %. FASTPlaqueTB gave better clinical performance with urine samples than with sputum samples (sensitivity, specificity and overall accuracy were 100 % with urine samples and 64, 93 and 84 % with sputum samples). The 100 % sensitivity of FASTPlaqueTB was higher than that of the corresponding values for PCR (67 %) with urine samples. In conclusion, FASTPlaqueTB proved to be sensitive, cheap relative to the PCR and rapid. It is able to detect M. tuberculosis in clinical samples within 1 day, reducing the time to diagnosis in comparison with culture.

DETECTING MYCOBACTERIUM TUBERCULOSIS RAPIDLY AND MYCOBACTERIUM TUBERCULOSIS STRAINS WITHOUT IS6110 SEQUENCE BY PCR ASSAY

2012 ◽  
pp. 15-19
Author(s):  
Thi Chau Anh Nguyen ◽  
Hoang Bach Nguyen ◽  
Hai Duong Huynh ◽  
Nu Xuan Thanh Le ◽  
Xuan Cuong Le ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
16S Rdna ◽  
False Negative ◽  
Clinical Samples ◽  
Tuberculosis Complex ◽  
Pcr Assay ◽  
Complex Objects ◽  
Method Performance ◽  
Gene Coding ◽  
16S Rdna Pcr

Background: The Nested IS6110 PCR is used for detecting tuberculosis, however IS6110 sequence is not present in the genome of all strains of M.tuberculosis, the result may be false negative. The gene coding 16S ribosome always contains a short sequence specific to M. tuberculosis complex. Objects: Performance of the 16S Real-time PCR to detect M. tuberculosis and combining to the nested IS6110 PCR to determine the rate of Mtb strains without IS6110 from clinical samples. Materials and method: Performance of 16S rDNA PCR by commercial kit of Viet A Inc. for all 480 samples, the samples which were positive with the 16S rDNA PCR were retested in IS6110 PCR assay by in-house kit. Results: The Realtime 16S rDNA PCR detected 258 cases (53.8%) of tuberculosis. There were 3 (1.2 %) M. tuberculosis strains which do not harbor IS6110 sequence in genome. Conclusion: The IS6110 nested PCR can be applied more widely than the 16S rDNA realtime PCR. In case of using IS6110 PCR assay, results may show a low proportion of false negative. Combining 16S rDNA PCR with the IS6110 based PCR allowed detection of deletion of IS6110 sequence in M. tuberculosis isolates.

scholarly journals Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Phelim Bradley ◽  
N. Claire Gordon ◽  
Timothy M. Walker ◽  
Laura Dunn ◽  
Simon Heys ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Mycobacterium Tuberculosis ◽  
Sequence Data ◽  
Error Rates ◽  
Graph Representation ◽  
Clinical Samples ◽  
Resistant Bacteria ◽  
Independent Validation ◽  
Validation Set ◽  
Sensitivity Specificity

Abstract The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for Staphylococcus aureus and Mycobacterium tuberculosis in a software package (‘Mykrobe predictor’) that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For S. aureus, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, n=470). For M. tuberculosis, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, n=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes.

Development of a LUX real-time PCR for the detection and quantification of human herpesvirus 7

2009 ◽  
Vol 55 (3) ◽  
pp. 319-325 ◽  
Author(s):  
Massimiliano Bergallo ◽  
Cristina Costa ◽  
Maria Elena Terlizzi ◽  
Francesca Sidoti ◽  
Samuela Margio ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Primary Infection ◽  
Latent Infection ◽  
Dynamic Range ◽  
Human Herpesvirus ◽  
Clinical Samples ◽  
House Light ◽  
Pcr Assay ◽  
Sensitivity Specificity

Human herpesvirus 7 is a highly seroprevalent β-herpesvirus that, following primary infection, remains latent in CD4+ T cells and determines a persistent rather than a latent infection in various tissues and organs, including the lung and skin. This paper describes the development of an in-house light upon extension real-time PCR assay for quantification of human herpesvirus 7 DNA in clinical samples. The efficiency, sensitivity, specificity, inter- and intra-assay variability, and dynamic range have been determined. Subsequently, the assay has been validated by evaluating the human herpesvirus 7 load in bronchoalveolar lavages and skin specimens, chosen as 2 persistency sites, from healthy and pathological individuals. The real-time PCR assay developed in this study could be a useful tool to detect and quantify human herpesvirus 7 DNA in different clinical specimens to elucidate its epidemiological and pathogenic roles.

scholarly journals Toward point-of-care diagnostics of Candida auris

2020 ◽  
Author(s):  
Geoffrey Mulberry ◽  
Sudha Chaturvedi ◽  
Vishnu Chaturvedi ◽  
Brian N. Kim
Keyword(s):  
New York ◽  
Real Time ◽  
Real Time Pcr ◽  
Positive Impact ◽  
Point Of Care ◽  
Low Cost ◽  
High Sensitivity ◽  
Clinical Samples ◽  
Pcr Assay ◽  
Candida Auris

AbstractCandida auris is a multidrug-resistant yeast that presents global health threat for the hospitalized patients. Early diagnostic of C. auris is crucial in control, prevention, and treatment. Candida auris is difficult to identify with standard laboratory methods and often can be misidentified leading to inappropriate management. A newly-devised real-time PCR assay played an important role in the ongoing investigation of the C. auris outbreak in New York metropolitan area. The assay can rapidly detect C. auris DNA in surveillance and clinical samples with high sensitivity and specificity, and also useful for confirmation of C. auris cultures. Despite its positive impact, the real-time PCR assay is difficult to deploy at frontline laboratories due to high-complexity set-up and operation. Using a low-cost handheld real-time PCR device, we show that the C. auris can potentially be identified in a low-complexity assay without the need for high-cost equipment. An implementation of low-cost real-time PCR device in hospitals and healthcare facilities is likely to accelerate the diagnosis of C. auris and for control of the global epidemic.

scholarly journals Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay

2020 ◽  
Author(s):  
James P. Broughton ◽  
Xianding Deng ◽  
Guixia Yu ◽  
Clare L. Fasching ◽  
Jasmeet Singh ◽  
...  
Keyword(s):  
Low Cost ◽  
Lateral Flow ◽  
Lateral Flow Assay ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Pcr Assay ◽  
The Us ◽  
Comparable Performance ◽  
Novel Coronavirus ◽  
Reference Samples

ABSTRACTAn outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report the development of SARS-CoV-2 DETECTR, a rapid (∼30 min), low-cost, and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated this method using contrived reference samples and clinical samples from infected US patients and demonstrated comparable performance to the US CDC SARS-CoV-2 real-time RT-PCR assay.

scholarly journals Evaluation of the Abbott LCx Mycobacterium tuberculosis Assay for Direct Detection of Mycobacterium tuberculosis Complex in Human Samples

1999 ◽  
Vol 37 (1) ◽  
pp. 229-232 ◽  
Author(s):  
Maria Grazia Garrino ◽  
Youri Glupczynski ◽  
Josiane Degraux ◽  
Henri Nizet ◽  
Michel Delmée
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Direct Detection ◽  
Clinical Samples ◽  
Culture Methods ◽  
Predictive Values ◽  
Direct Microscopy ◽  
Standard Culture ◽  
Small Gain ◽  
Clinical Interest ◽  
Sensitivity Specificity

Seven hundred thirty-seven clinical samples from 460 patients were processed for direct detection of Mycobacterium tuberculosis complex by a semiautomated ligase chain reaction commercial assay, the LCx Mycobacterium tuberculosis Assay (LCx assay) from Abbott Laboratories. Results were compared to those of direct microscopy and standard microbiological culture. Of 26 patients (5.7%) with a culture positive for M. tuberculosis, 22 (84.6%) were found positive by the LCx assay. The sensitivity of the LCx assay was 98% for smear-positive samples and 27% for smear-negative samples. With an overall culture positivity rate forM. tuberculosis of 8.3% (61 of 737 samples) and after resolution of discrepant results according to clinical data, the sensitivity, specificity, and positive and negative predictive values of the LCx assay were 78, 100, 95, and 98%, respectively, compared to 85, 100, 100, and 98%, respectively, for culture and 67, 99, 87, and 97%, respectively, for acid-fast staining. In conclusion, the LCx assay proved satisfactory and appears to be an easy-to-use 1-day test which must be used with standard culture methods but can considerably reduce diagnosis time versus culture. However, its clinical interest appears to be limited in our population with low mycobacterial prevalence because of its cost considering the small gain in sensitivity versus direct microscopy.

Monochrome LightCycler PCR assay for detection and quantification of five common species of Candida and Aspergillus

2005 ◽  
Vol 54 (3) ◽  
pp. 243-248 ◽  
Author(s):  
Rong Bu ◽  
Rajeev K Sathiapalan ◽  
Muna M Ibrahim ◽  
Ibrahim Al-Mohsen ◽  
Edna Almodavar ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Fungal Pathogens ◽  
Low Cost ◽  
False Negative ◽  
Common Species ◽  
Fungal Species ◽  
Clinical Samples ◽  
Pcr Assay ◽  
Negative Results ◽  
Identification And Quantification

Invasive fungal pathogens, especially in immunocompromised hosts, can result in life-threatening infections. Current laboratory/radiological methods for fungal identification are time-consuming and lack sensitivity and specificity. A monochrome, multiplex, real-time PCR assay for the identification and quantification of Candida albicans, Candida krusei, Candida tropicalis, Aspergillus flavus and Aspergillus fumigatus is described here. Detection of each of these fungi was specific and demonstrated 100 % concordance with biochemical/culture identification in all 60 isolates tested. Samples from 16 febrile neutropenic patients with haematological malignancies were also analysed and the utility of the assay in clinical samples was reconfirmed without false-negative results. The sensitivity of this assay was 0.1 pg fungal genomic DNA, corresponding to three cells, for C. albicans, C. krusei, C. tropicalis and A. flavus, and 0.01 pg fungal genomic DNA, i.e. less than one cell, for A. fumigatus. The analysis allows a low-cost, simple, rapid and sensitive alternative for clinical identification and quantification of these five common fungal species.

scholarly journals Noninferiority and Equivalence Evaluation of Clinical Performance among Computed Radiography, Film, and Digitized Film for Telemammography Services

2016 ◽  
Vol 2016 ◽  
pp. 1-12 ◽  
Author(s):  
Antonio J. Salazar ◽  
Javier A. Romero ◽  
Oscar A. Bernal ◽  
Angela P. Moreno ◽  
Sofía C. Velasco ◽  
...  
Keyword(s):  
Clinical Performance ◽  
Underserved Populations ◽  
Computed Radiography ◽  
Low Cost ◽  
Digital Camera ◽  
Mean Values ◽  
Receiver Operating Characteristic Curves ◽  
Screening Programs ◽  
Film Digitizer ◽  
Sensitivity Specificity

Objective.The aim of this study was to evaluate and compare the clinical performance of different alternatives to implement low-cost screening telemammography. We compared computed radiography, film printed images, and digitized films produced with a specialized film digitizer and a digital camera.Material and Methods.The ethics committee of our institution approved this study. We assessed the equivalence of the clinical performance of observers for cancer detection. The factorial design included 70 screening patients, four technological alternatives, and cases interpreted by seven radiologists, for a total of 1,960 observations. The variables evaluated were the positive predictive value (PPV), accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curves (AUC).Result. The mean values for the observed variables were as follows: accuracy ranged from 0.77 to 0.82, the PPV ranged from 0.67 to 0.68, sensitivity ranged from 0.64 to 0.74, specificity ranged from 0.87 to 0.90, and the AUC ranged from 0.87 to 0.90. At a difference of 0.1 to claim equivalence, all alternatives were equivalent for all variables.Conclusion.Our findings suggest that telemammography screening programs may be provided to underserved populations at a low cost, using a film digitizer or a digital camera.

scholarly journals Development and performance evaluation of a low-cost in-house rRT-PCR assay in Ecuador for the detection of SARS-CoV-2

2021 ◽  
Author(s):  
Marco Salinas ◽  
Diana Aguirre ◽  
David De la Torre ◽  
Jorge Pérez-Galarza ◽  
Ronny Pibaque ◽  
...  
Keyword(s):  
Internal Control ◽  
Low Income ◽  
Clinical Performance ◽  
Low Cost ◽  
Viral Envelope ◽  
Low Income Countries ◽  
Pcr Assay ◽  
Gene Target ◽  
P Gene ◽  
And Performance

Antecedents: Ecuador has had the greatest fatality rate from Coronavirus (COVID-19) in South America during the SARS-CoV-2 pandemic. To control the pandemic, it is necessary to test as much population as possible to prevent the spread of the SARS-CoV-2 infection. For the Ecuadorian population, accessing a PCR test is challenging, since commercial screening kits tend to be expensive. Objective: the objective of this study was to develop an in-house duplex rRT-PCR protocol for the detection of SARS-CoV-2 that contributes to the screening while keeping quality and low testing costs. Results: An in-house duplex rRT-PCR protocol based on the viral envelope (E) gene target of SARS-CoV-2 and a human ribonuclease P gene (RP) as an internal control is reported. The protocol was optimized to obtain primers E with an efficiency of up to 94.45% and detection of 100% of SARS-CoV-2 up to 15 copies per uL. The clinical performance was determined by a sensibility of 93.8% and specificity of 98.3%. Conclusion: we developed, standardized, and validated a low-cost, sensitive in-house duplex rRT-PCR assay that may be utilized in low-income countries.

Sign in / Sign up

Export Citation Format

Share Document