scholarly journals Validation and Implementation of a Diagnostic Algorithm for DNA Detection ofBordetella pertussis,B. parapertussis, andB. holmesiiin a Pediatric Referral Hospital in Barcelona, Spain

2018 ◽  
Vol 57 (1) ◽  
Author(s):  
Ana Valero-Rello ◽  
Desiree Henares ◽  
Lesly Acosta ◽  
Mireia Jane ◽  
Iolanda Jordan ◽  
...  
Keyword(s):  
Internal Control ◽  
Whooping Cough ◽  
Diagnostic Algorithm ◽  
Clinical Samples ◽  
Analytical Validation ◽  
Content Type ◽  
Detection And Identification ◽  
Ofbordetella Pertussis ◽  
Lower Limits

ABSTRACTThis study aimed to validate a comprehensive diagnostic protocol based on real-time PCR for the rapid detection and identification ofBordetella pertussis,Bordetella parapertussis, andBordetella holmesii, as well as its implementation in the diagnostic routine of a reference children’s hospital. The new algorithm included a triplex quantitative PCR (qPCR) targeting IS481gene (inB. pertussis,B. holmesii, and someBordetella bronchisepticastrains), pIS1001(B. parapertussis-specific) andrnaseP as the human internal control. Two confirmatory singleplex tests forB. pertussis(ptxA-Pr) andB. holmesii(hIS1001) were performed if IS481was positive. Analytical validation included determination of linear range, linearity, efficiency, precision, sensitivity, and a reference panel with clinical samples. Once validated, the new algorithm was prospectively implemented in children with clinical suspicion of whooping cough presenting to Hospital Sant Joan de Deu (Barcelona, Spain) over 12 months. Lower limits of detection obtained were 4.4, 13.9, and 27.3 genomic equivalents/ml of sample for IS481(onB. pertussis), pIS1001and hIS1001, and 777.9 forptxA-Pr. qPCR efficiencies ranged from 86.0% to 96.9%. Intra- and interassay variabilities were <3% and <5%, respectively. Among 566 samples analyzed,B. pertussis,B. holmesii, andB. parapertussiswere detected in 11.1%, 0.9% (only in females >4 years old), and 0.2% of samples, respectively. The new algorithm proved to be a useful microbiological diagnostic tool for whooping cough, demonstrating a low rate of other non-pertussisBordetellaspecies in our surveilled area.

scholarly journals Development of a DNA Microarray Method for Detection and Identification of All 15 Distinct O-Antigen Forms of Legionella pneumophila

2013 ◽  
Vol 79 (21) ◽  
pp. 6647-6654 ◽  
Author(s):  
Boyang Cao ◽  
Fangfang Yao ◽  
Xiangqian Liu ◽  
Lu Feng ◽  
Lei Wang
Keyword(s):  
Dna Microarray ◽  
Legionella Pneumophila ◽  
Detection Sensitivity ◽  
Immunological Methods ◽  
Clinical Samples ◽  
Content Type ◽  
O Antigen ◽  
Detection And Identification ◽  
Legionnaires Disease ◽  
Reference Strains

ABSTRACTLegionellais ubiquitous in many environments. At least 50 species and 70 serogroups of the Gram-negative bacterium have been identified. Of the 50 species, 20 are pathogenic, andLegionella pneumophilais responsible for the great majority (approximately 90%) of the Legionnaires' disease cases that occur. Furthermore, of the 15L. pneumophilaserogroups identified, O1 alone causes more than 84% of the Legionnaires' disease cases that occur worldwide. Rapid and reliable assays for the detection and identification ofL. pneumophilain water, environmental, and clinical samples are in great demand.L. pneumophilabacteria are traditionally identified by their O antigens by immunological methods. We have recently developed an O serogroup-specific DNA microarray for the detection of all 15 distinct O-antigen forms ofL. pneumophila, including serogroups O1 to O15. A total of 35 strains were used to verify the specificity of the microarray, including 15L. pneumophilaO-antigen standard reference strains and sevenL. pneumophilaclinical isolates as target strains, seven reference strains of other non-pneumophila Legionellaspecies as closely related strains, and six non-Legionellabacterial species as nonrelated strains. The detection sensitivity was 1 ng of genomic DNA or 0.4 CFU/ml in water samples with filter enrichment and plate culturing. This study demonstrated that the microarray allows specific, sensitive, and reproducible detection ofL. pneumophilaserogroups. To the best of our knowledge, this is the first report of a microarray serotyping method for all 15 distinct O-antigen forms ofL. pneumophila.

scholarly journals Pertussis Serodiagnosis in Belgium from 1990 to 2009

2011 ◽  
Vol 18 (4) ◽  
pp. 588-594 ◽  
Author(s):  
Muriel Vincent ◽  
Caroline Rodeghiero ◽  
Romain Eylenbosch ◽  
Yvan Mans ◽  
Jeannine Swalus-Steenhouwer ◽  
...  
Keyword(s):  
Potential Role ◽  
Whooping Cough ◽  
Age Groups ◽  
Childhood Vaccination ◽  
Clinical Samples ◽  
Content Type ◽  
The Mean ◽  
Children And Young Adolescents ◽  
Vaccination Campaigns

ABSTRACTDiagnosis of pertussis by culture and PCR is most sensitive when performed on nasopharyngeal specimens collected <2 weeks and <3 weeks, respectively, after the onset of clinical disease. Conversely, serological testing allows the diagnosis of patients (mostly adults) with less typical whooping cough symptoms, for whom clinical samples are often collected at later time points. Here, we report on a 20-year serodiagnostic survey of pertussis in Belgium from 1990 to 2009. In total, 13,163 patients were analyzed forBordetella pertussis-specific antibodies by agglutination, complement fixation, immunofluorescence, and ELISA. The number of positive pertussis cases detected by serodiagnosis ranged between 50 and 150 annually. The mean age of positive cases increased from 9.9 years in 1990 to 33.9 years in 2009. Whereas from 1990 to 2003, children and young adolescents made up the majority of cases, from 2004 onwards, cases were detected in all age groups and the distribution became bimodal, with a first peak at the age of 10 to 20 years and a second at the age of 35 to 50 years. In contrast, patients diagnosed since 2001 by PCR and/or culture were mostly children younger than 1 year of age. Despite extensive childhood vaccination campaigns, whooping cough is still present in Belgium. Our findings confirm the potential role of adults in the continued transmission of pertussis and strongly warrant booster or cocoon vaccinations in older age groups.

scholarly journals Development of a DNA Microarray for Molecular Identification of All 46 Salmonella O Serogroups

2013 ◽  
Vol 79 (11) ◽  
pp. 3392-3399 ◽  
Author(s):  
Dan Guo ◽  
Bin Liu ◽  
Fenxia Liu ◽  
Boyang Cao ◽  
Min Chen ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Bacterial Species ◽  
Rapid Identification ◽  
Detection Sensitivity ◽  
Epidemiological Surveillance ◽  
Disease Assessment ◽  
Content Type ◽  
Detection And Identification ◽  
Food Borne

ABSTRACTSalmonellais a major cause of food-borne disease in many countries. Serotype determination ofSalmonellais important for disease assessment, infection control, and epidemiological surveillance. In this study, a microarray system that targets the O antigen-specific genes was developed for simultaneously detecting and identifying all 46SalmonellaO serogroups. Of these, 40 serogroups can be confidently identified, and the remaining 6, in three pairs (serogroups O67 and B, E1 and E4, and A and D1), need to be further distinguished from each other using PCR methods or conventional serotyping methods. The microarray was shown to be highly specific when evaluated against 293Salmonellastrains, 186Shigellastrains, representativeEscherichia colistrains, and 10 strains of other bacterial species. The assay correctly identified 288 (98%) of theSalmonellastrains. The detection sensitivity was determined to be 50 ng genomic DNA per sample. By testing simulated samples in a tomato background, 2 to 8 CFU per gram inoculated could be detected after enrichment. This newly developed microarray assay is the first molecular protocol that can be used for the comprehensive detection and identification of all 46SalmonellaO serogroups. Compared to the traditional serogrouping method, the microarray provides a reliable, high-throughput, and sensitive approach that can be used for rapid identification of multipleSalmonellaO serogroups simultaneously.

A Rapid Method for Determination of Buprenorphine and Norbuprenorphine in Urine by UPLC-MS/MS

2020 ◽  
Vol 16 ◽  
Author(s):  
Aykut Kul ◽  
Murat Ozdemir ◽  
Selma Ozilhan ◽  
Olcay Sagirli
Keyword(s):  
Forensic Science ◽  
Rapid Method ◽  
Proficiency Testing ◽  
Mass Spectrometer ◽  
Illicit Market ◽  
Analysis Methods ◽  
Accuracy And Precision ◽  
Lower Limits

Background: Buprenorphine is quite common in the illicit market. Buprenorphine-containing drugs abuse is frequently encountered in patients. The analysis methods used to determine the abuse of buprenorphine and norbuprenorphine are important for forensic science. Buprenorphine is metabolized to norbuprenorphine by the liver. Objective: Therefore, the determination of buprenorphine and norbuprenorphine in urine is one of the methods to determine the abuse of buprenorphine. Methods: In this study, we have developed a precise, simple, and rapid ultra-performance liquid chromatographytandem mass spectrometer method for the determination of buprenorphine and norbuprenorphine simultaneously. Results: The developed method was validated in terms of selectivity and linearity, which was in the range of 9–1800 ng/mL for both buprenorphine and norbuprenorphine. The intra-assay and inter-assay accuracy and precision were found within acceptable limits of the EMA guideline. Lower limits of quantitation were 9 ng/mL for both buprenorphine and norbuprenorphine. Conclusion: The developed method was successfully applied for the determination of both analytes in the proficiency testing samples.

scholarly journals Mutations in fbiD (Rv2983) as a Novel Determinant of Resistance to Pretomanid and Delamanid in Mycobacterium tuberculosis

2020 ◽  
Vol 65 (1) ◽  
pp. e01948-20
Author(s):  
Dalin Rifat ◽  
Si-Yang Li ◽  
Thomas Ioerger ◽  
Keshav Shah ◽  
Jean-Philippe Lanoix ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Clinical Evidence ◽  
Clinical Samples ◽  
Loss Of Function ◽  
Wild Type ◽  
Content Type ◽  
Solid Media ◽  
High Level ◽  
Level Resistance

ABSTRACTThe nitroimidazole prodrugs delamanid and pretomanid comprise one of only two new antimicrobial classes approved to treat tuberculosis (TB) in 50 years. Prior in vitro studies suggest a relatively low barrier to nitroimidazole resistance in Mycobacterium tuberculosis, but clinical evidence is limited to date. We selected pretomanid-resistant M. tuberculosis mutants in two mouse models of TB using a range of pretomanid doses. The frequency of spontaneous resistance was approximately 10−5 CFU. Whole-genome sequencing of 161 resistant isolates from 47 mice revealed 99 unique mutations, of which 91% occurred in 1 of 5 genes previously associated with nitroimidazole activation and resistance, namely, fbiC (56%), fbiA (15%), ddn (12%), fgd (4%), and fbiB (4%). Nearly all mutations were unique to a single mouse and not previously identified. The remaining 9% of resistant mutants harbored mutations in Rv2983 (fbiD), a gene not previously associated with nitroimidazole resistance but recently shown to be a guanylyltransferase necessary for cofactor F420 synthesis. Most mutants exhibited high-level resistance to pretomanid and delamanid, although Rv2983 and fbiB mutants exhibited high-level pretomanid resistance but relatively small changes in delamanid susceptibility. Complementing an Rv2983 mutant with wild-type Rv2983 restored susceptibility to pretomanid and delamanid. By quantifying intracellular F420 and its precursor Fo in overexpressing and loss-of-function mutants, we provide further evidence that Rv2983 is necessary for F420 biosynthesis. Finally, Rv2983 mutants and other F420H2-deficient mutants displayed hypersusceptibility to some antibiotics and to concentrations of malachite green found in solid media used to isolate and propagate mycobacteria from clinical samples.

scholarly journals Molecular Characterisation and Phylogenetic Analysis of Dermatophytic Fungi Isolated from Tinea Capitis in Northwest Nigeria Using Sequence of the 28S rRNA

2021 ◽  
Vol 12 (3) ◽  
pp. 646-655
Author(s):  
Hussain Yahaya Ungo-kore ◽  
Joseph Olorunmola Ehinmidu ◽  
Josiah Ademola Onaolapo ◽  
Olayeni Stephen Olonitola
Keyword(s):  
Phylogenetic Analysis ◽  
Tinea Capitis ◽  
28S Rdna ◽  
Clinical Samples ◽  
28S Rrna ◽  
Trichophyton Tonsurans ◽  
Detection And Identification ◽  
Microsporum Audouinii ◽  
Trichophyton Simii ◽  
Dermatophyte Species

The detection and identification of fungal DNA from clinical samples is one of the fundamental approaches in biomedicine. The incidence, distribution, and control of dermatophytes has progress significantly and the use of phylogenetic species concepts based on rRNA regions have enhanced the taxonomy of dermatophyte species; however, the use of 28S rDNA genes has certain limitations. This gene has been used in dermatophyte taxonomy with limited enumeration; we appraised the sequence disparity within and among groups of the species, the gene ranking in identification, phylogenetic analysis, and taxonomy of 32 strains of eight dermatophyte species. In this study, a set of primers was adopted to amplify the target followed by a partial sequencing of the rDNA. The utilization of a pairwise nucleotide differentiation, an affinity was observed among eight dermatophyte species, with disparity among species ranging from 0 to 197 base pair (bp). Intra-species bp differences were found within strains of Trichophyton eriotrephon, Trichophyton bullosum, Trichophyton simii (Trichophyton genus), Microsporum audouinii, and Trichophyton tonsurans (Microsporum and Trichophyton genus, respectively); however, only some strains of Trichophyton eriotrephon were found to be invariant having three genotypes. Trichophyton tonsurans exhibited most intra-species variability. The characterization and construction of a phylogenetic tree of 28S rDNA gene on dermatophyte species provide a bedrock of an additional finding of connections between species. However, 28S rRNA capture provides a novel method of effective and sensitive detection of dermatophytes lodged in human skin scale. We report for the first time the emergence of T. eriotrephon, T. bullosum, T. simii, T. benhamiae, and Ctenomyces serratus dermatophytes from Tinea capitis in Nigeria.

scholarly journals Development of new spectrophotometric method for estimation of tenofovir disoproxil fumarate using MBTH reagent

2015 ◽  
Vol 4 (4) ◽  
pp. 378-381 ◽  
Author(s):  
Mannem Sri Varsha ◽  
N. Raghavendra Babu ◽  
Yenumula Padmavathi ◽  
P. Ravi Kumar
Keyword(s):  
Tenofovir Disoproxil Fumarate ◽  
Visible Region ◽  
Pharmaceutical Formulations ◽  
Pharmaceutical Journal ◽  
Specific Procedure ◽  
Analytical Validation ◽  
Pharmaceutical Dosage Forms ◽  
Secondary Amine Group ◽  
Validation Procedure

A new simple, sensitive and specific procedure has been developed for determination of tenofovir disoproxil fumarate in bulk and pharmaceutical dosage forms using MBTH reagent. The purpose of this analytical validation procedure is to validate it by laboratory experiments to prove that the method meets the minimum standards for laboratory use. 3-methyl-2-bezothiazoline hydrazone reacts with the secondary amine group of tenofovir in the presence of oxidizing agent, ferric chloride. The resulting apple green coloured chromogen when measured spectrophotometrically in visible region (i.e., 400-800nm) shows a maximum absorbance at 626.5nm. This method can be successfully applied for the determination of drug content in pharmaceutical formulations. The results of analysis have been validated statistically.DOI: http://dx.doi.org/10.3329/icpj.v4i4.22620 International Current Pharmaceutical Journal, March 2015, 4(4): 378-381 

scholarly journals Essential properties and pitfalls of colorimetric Reverse Transcription Loop-mediated Isothermal Amplification as a point-of-care test for SARS-CoV-2 diagnosis

2021 ◽  
Vol 27 (1) ◽  
Author(s):  
Bruna de Oliveira Coelho ◽  
Heloisa Bruna Soligo Sanchuki ◽  
Dalila Luciola Zanette ◽  
Jeanine Marie Nardin ◽  
Hugo Manuel Paz Morales ◽  
...  
Keyword(s):  
Viral Load ◽  
Internal Control ◽  
Reverse Transcription ◽  
Color Change ◽  
Point Of Care ◽  
Colorimetric Detection ◽  
False Negative ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Loop Mediated Isothermal Amplification

Abstract Background SARS-CoV-2 Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) colorimetric detection is a sensitive and specific point-of-care molecular biology technique used to detect the virus in only 30 min. In this manuscript we have described a few nuances of the technique still not properly described in the literature: the presence of three colors clusters; the correlation of the viral load with the color change; and the importance of using an internal control to avoid false-negative results. Methods To achieve these findings, we performed colorimetric RT-LAMP assays of 466 SARS-CoV-2 RT-qPCR validated clinical samples, with color quantification measured at 434 nm and 560 nm. Results First we determinate a sensitivity of 93.8% and specificity of 90.4%. In addition to the pink (negative) and yellow (positive) produced colors, we report for the first time the presence of an orange color cluster that may lead to wrong diagnosis. We also demonstrated using RT-qPCR and RT-LAMP that low viral loads are related to Ct values > 30, resulting in orange colors. We also demonstrated that the diagnosis of COVID-19 by colorimetric RT-LAMP is efficient until the fifth symptoms day when the viral load is still relatively high. Conclusion This study reports properties and indications for colorimetric RT-LAMP as point-of-care for SARS-CoV-2 diagnostic, reducing false results, interpretations and optimizing molecular diagnostics tests application.

Locating complex eigenvalues for analytical eddy-current models used to detect flaws

2019 ◽  
Vol 38 (6) ◽  
pp. 1800-1809
Author(s):  
Grzegorz Tytko ◽  
Łukasz Dawidowski
Keyword(s):  
Eddy Current ◽  
Design Methodology ◽  
Complex Function ◽  
Precise Determination ◽  
Argument Principle ◽  
Content Type ◽  
Conductive Material ◽  
Complex Roots ◽  
Complex Eigenvalues

Purpose Discrete eigenvalues occur in eddy current problems in which the solution domain was truncated on its edge. In case of conductive material with a hole, the eigenvalues are complex numbers. Their computation consists of finding complex roots of a complex function that satisfies the electromagnetic interface conditions. The purpose of this paper is to present a method of computing complex eigenvalues that are roots of such a function. Design/methodology/approach The proposed approach involves precise determination of regions in which the roots are found and applying sets of initial points, as well as the Cauchy argument principle to calculate them. Findings The elaborated algorithm was implemented in Matlab and the obtained results were verified using Newton’s method and the fsolve procedure. Both in the case of magnetic and nonmagnetic materials, such a solution was the only one that did not skip any of the eigenvalues, obtaining the results in the shortest time. Originality/value The paper presents a new effective method of locating complex eigenvalues for analytical solutions of eddy current problems containing a conductive material with a hole.

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