scholarly journals The Laboratory Diagnosis ofNeisseria gonorrhoeae

2005 ◽  
Vol 16 (1) ◽  
pp. 15-25 ◽  
Author(s):  
Lai-King Ng ◽  
Irene E Martin
Keyword(s):  
Nucleic Acid ◽  
Diagnostic Testing ◽  
Laboratory Diagnosis ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Biochemical Tests ◽  
Culture Methods ◽  
Gene Target ◽  
Clinical Specimens ◽  
Confirmatory Tests

The present article describes the laboratory diagnosis ofNeisseria gonorrhoeaeby culturing of the organism from different types of clinical specimens followed by confirmatory tests. The success of culture methods requires good quality collection and transport of clinical specimens. The present guide describes the media requirements and cultural conditions forN gonorrhoeaegrowth and the characteristics for a presumptive identification ofN gonorrhoeae. Confirmatory tests include biochemical tests, chromogenic enzyme substrate tests, immunoassays and nucleic acid methods. Nucleic acid detection methods include either amplification-based methods or nonamplification tests, and are increasingly used in clinical laboratories where a viable culture is not possible to obtain. Nucleic acid methods can also be used to detect the presence of low numbers in a specimen. Nucleic acid detection methods need confirmation with another amplification method or gene target. Controls must be included to ensure true positive and negative results, and to rule out nucleic acid contamination. Monitoring of antimicrobial susceptibilities ofN gonorrhoeaeis important to investigate treatment failure and to evaluate the efficacy of currently recommended therapies. Many methods for the characterization ofN gonorrhoeaerequire cultures. The useful typing methods for determining strain relatedness include auxotyping, serotyping, plasmid profile analysis, DNA sequencing of theporBgene and pulsed-field gel electrophoresis. Quality assurance programs for diagnostic testing and antimicrobial susceptibility testing is reviewed.

scholarly journals Different Laboratory Diagnosis methods of COVID-19: A Systematic Review

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Navid Omidifar ◽  
Kamran Bagheri Lankarani ◽  
Mohsen Moghadami ◽  
Mansoureh Shokripour ◽  
Mostafa Chashmpoosh ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Laboratory Diagnosis ◽  
Diagnostic Techniques ◽  
Disease Spread ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Laboratory Equipment ◽  
Reactive Protein ◽  
Pcr Method ◽  
Conferences And Congresses

: The virus causing COVID-19 disease is known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease spread rapidly and was transmitted like a contagious disease throughout China, and then it gradually spread in other parts of the world. Accordingly, the rapid and accurate detection of the SARS-CoV-2 virus plays an essential role in selecting timely treatments, saving lives, and preventing the spread of the disease. This study summarizes the methods used to identify coronavirus nucleic acid. The effectiveness of coronavirus nucleic acid detection kits by different samples and the performance of other diagnostic techniques are also addressed in this study. We searched Embase, Google Scholar, MEDLINE, Web of Science, Scopus, and PubMed databases as well as the references of all relevant articles in English published during 2019 - 2020 using keywords related to COVID-19, detection kits, and respiratory failure and proceedings from relevant conferences and congresses. The authors collected the relevant reports, and each of the authors independently reviewed the data published in different studies. The results of previous studies indicated that the diagnosis methods of the COVID-19 disease are the RT-PCR method, ELISA kits, quick tests, white blood cell count, C-reactive protein (CRP) levels, other laboratory factors and antigenic detection methods. Given the sensitivity and specificity of these methods at different periods using different samples, the disease interpretation can be performed accurately. The findings showed that proper laboratory equipment and appropriate laboratory kits are necessary for the rapid and precise identification of COVID-19.

scholarly journals The Laboratory Diagnosis ofHaemophilus ducreyi

2005 ◽  
Vol 16 (1) ◽  
pp. 31-34 ◽  
Author(s):  
Michelle Alfa
Keyword(s):  
Diagnostic Testing ◽  
Laboratory Diagnosis ◽  
Primary Method ◽  
Sample Collection ◽  
Culture Methods ◽  
Transmitted Infection ◽  
Diagnostic Laboratory ◽  
Sexually Transmitted ◽  
Alternative Approaches ◽  
Genetic Amplification

Chancroid is a sexually transmitted infection caused byHaemophilus ducreyi. This fastidious, Gram-negative coccobacilli dies rapidly outside the human host, making diagnostic testing using culture methods difficult. This genital ulcer infection is not common in Canada and, therefore, can often be misdiagnosed. The objective of the present paper is to provide practical approaches for the diagnosis of chancroid in Canadian patients where the prevalence of this infection is low. Issues related to sample collection, sample transport and available diagnostic tests are reviewed, and several alternative approaches are outlined. Although antigen detection, serology and genetic amplification methods have all been reported forH ducreyi, none are commercially available. Culture is still the primary method available to most laboratories. However, the special media necessary for direct bedside inoculation is often not available; therefore, communication with the diagnostic laboratory and rapid specimen transport are essential when chancroid is suspected

scholarly journals Development and detection of genetically modified crops

2020 ◽  
Vol 145 ◽  
pp. 01013
Author(s):  
Zhao Yu-jia ◽  
Fan Pei-lei ◽  
Liang Liang ◽  
Liu Yin-yin ◽  
Zhao Hai-bo ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Genetically Modified ◽  
Genetically Modified Crops ◽  
Detection Methods ◽  
Social Benefits ◽  
Nucleic Acid Detection ◽  
Genetically Modified Crop ◽  
The World ◽  
The Difference

Genetically modified crops (GMCs) have been known for the excellent qualities. The commercializing of GMCs has taken great economic and social benefits. However, the bio-security of GMCs was still an issue. To solve this problem, countries around the world were constantly strengthening regulations on planting, processing and detecting of GMCs. This paper reviewed the development of commercialization and detection of GMCs. The difference between protein and nucleic acid detection methods of genetically modified crop was further discussed. This paper will provide new insights for the application of genetically modified crops.

scholarly journals Optimize Clinical Laboratory Diagnosis of COVID-19 from Suspect Cases by Likelihood Ratio of SARS-CoV-2 IgM and IgG antibody

2020 ◽  
Author(s):  
Feng Yangchun
Keyword(s):  
Nucleic Acid ◽  
Likelihood Ratio ◽  
Posterior Probability ◽  
Clinical Laboratory ◽  
Laboratory Diagnosis ◽  
Antibody Detection ◽  
Nucleic Acid Detection ◽  
Igg Antibodies ◽  
Igg Antibody ◽  
Antibody Tests

ObjectiveTo optimize clinical laboratory diagnosis of COVID-19 from suspect cases by Likelihood Ratio of SARS-CoV-2 IgM and IgG antibody.MethodsBy reinterpreting the data in the article “Diagnostic Value of Combined Detection of Serum 2019 novel coronavirus IgM and IgG Antibodies in novel coronavirusin Infection”, the positive likelihood ratio of IgM and IgG antibody in diagnosis of COVID-19 (nucleic acid positive patients) was calculated, and the posterior probability of IgM and IgG antibodies and their tandem detection to diagnose was finally calculated.ResultsThe positive likelihood ratios of single IgM and IgG antibody were 18.50 and 12.65 respectively, and the posterior probabilities were 90.18% and 86.26% respectively. However, the posterior probability of the two antibodies tandem detection is 99.15%, which can give clinicians quantitative confidence in the diagnosis of COVID-19 from suspected cases. According to the results of this study, combining the advantages and disadvantages of nucleic acid detection and antibody detection, the clinical pathway for clinicians to diagnose COVID-19 is found.ConclusionFor suspected cases, IgM and IgG antibody tests should be firstly done at the same time. If the antibody tests are all positive, COVID-19 can be confirmed. If not, nucleic acid detection (one or more times) is performed, and in extreme cases, high-throughput viral genome sequencing is performed.

scholarly journals Rapidemic, a versatile and label-free DNAzyme-based platform for visual nucleic acid detection

2020 ◽  
Author(s):  
Marijn van den Brink ◽  
Sebastian T. Tandar ◽  
Tim A. P. van den Akker ◽  
Sinisha Jovikj ◽  
Violette Defourt ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Infectious Diseases ◽  
Detection Method ◽  
Point Of Care ◽  
Diagnostic Testing ◽  
Nucleic Acid Detection ◽  
Label Free ◽  
Strand Displacement Amplification ◽  
Sequence Detection ◽  
Accessible Point

AbstractIn the last three decades, there have been recurring outbreaks of infectious diseases, brought to light with the recent outbreak of coronavirus disease 2019 (COVID-19). Attempts to effectively contain the spread of infectious diseases have been hampered by the lack of rapidly adaptable, accurate, and accessible point-of-care diagnostic testing. In this study, we present a novel design of a label-free DNAzyme-based detection method called Rapidemic. This assay combines recombinase polymerase amplification (RPA) with linear strand-displacement amplification (LSDA) and guanine-quadruplex (GQ) DNAzyme-catalysed colour-changing reaction. The colorimetry basis of the signal readout omits the need for extensive instrumentation. Moreover, the primer-based sequence detection of RPA gives Rapidemic a potential to be rapidly adapted to target a new sequence. As a proof of concept, we developed the assay to detect isolated genomic DNA of Saccharomyces cerevisiae. The use of low-pH buffers and the optimization of the dilution rates from each preceding reaction to the next showed to be successful strategies to enable visible detection with this method. These findings demonstrate for the first time that a label-free DNAzyme-based detection method can be coupled to RPA and LSDA for nucleic acid detection.

scholarly journals Evaluation of seven different rapid methods for nucleic acid detection of SARS-COV-2 virus

2021 ◽  
Author(s):  
Sally Mahmoud ◽  
Esra Ibrahim ◽  
Subhashini Ganesan ◽  
Bhagyashree Thakre ◽  
Juliet Teddy ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Gold Standard ◽  
Large Scale ◽  
Virus Detection ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Test Accuracy ◽  
Rt Pcr ◽  
Rapid Methods ◽  
Kappa Value

Background In the current COVID-19 pandemic there is mass screening of SARS-CoV-2 happening round the world due to the extensive spread of the infections. There is a high demand for rapid diagnostic tests to expedite identification of cases and to facilitate early isolation and control spread. Hence this study evaluates seven different rapid nucleic acid detection assays that are commercially available for SARS- CoV- 2 virus detection. Methods Nasopharyngeal samples were collected from 4859 participants and were tested for SARS-CoV-2 virus by the gold standard RT-PCR method along with one of these seven rapid methods of detection. Evaluation of the rapid nucleic acid detection assays was done by comparing the results of these rapid methods with the gold standard RT-qPCR results for SARS-COV-2 detection. Results AQ-TOP had the highest sensitivity (98%) and strong kappa value of 0.943 followed by Genechecker and Abbot ID NOW. The POCKIT (ii RT-PCR) assay had the highest test accuracy of 99.29% followed by Genechecker and Cobas Liat. Atila iAMP showed the highest percentage of invalid reports (35.5%) followed by AQ-TOP with 6% and POCKIT with 3.7% of invalid reports. Conclusion Genechecker system, Abbott ID NOW and Cobas Liat, were found to have best performance and agreement when compared to the standard RT-PCR for COVID-19 detection. With further research, these rapid tests have the potential to be employed in large scale screening of COVID-19.

scholarly journals Assessment of the Diagnostic Ability of Four Detection Methods Using Three Sample Types of COVID-19 Patients

2021 ◽  
Vol 11 ◽  
Author(s):  
Fei Yu ◽  
Guoliang Xie ◽  
Shufa Zheng ◽  
Dongsheng Han ◽  
Jiaqi Bao ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Reverse Transcription ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Sample Type ◽  
Rt Pcr ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Oropharyngeal Swab ◽  
And Control

BackgroundViral nucleic acid detection is considered the gold standard for the diagnosis of coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2 infection. However, unsuitable sample types and laboratory detection kits/methods lead to misdiagnosis, which delays the prevention and control of the pandemic.MethodsWe compared four nucleic acid detection methods [two kinds of reverse transcription polymerase chain reactions (RT-PCR A: ORF1ab and N testing; RT-PCRB: only ORF1ab testing), reverse transcription recombinase aided amplification (RT-RAA) and droplet digital RT-PCR (dd-RT-PCR)] using 404 samples of 72 hospitalized COVID-19 patients, including oropharyngeal swab (OPS), nasopharyngeal swabs (NPS) and saliva after deep cough, to evaluate the best sample type and method for SARS-CoV-2 detection.ResultsAmong the four methods, dd-RT-PCR exhibited the highest positivity rate (93.0%), followed by RT-PCR B (91.2%) and RT-RAA (91.2%), while the positivity rate of RT-PCR A was only 71.9%. The viral load in OPS [24.90 copies/test (IQR 15.58-129.85)] was significantly lower than that in saliva [292.30 copies/test (IQR 20.20-8628.55)] and NPS [274.40 copies/test (IQR 33.10-2836.45)]. In addition, if OPS samples were tested alone by RT-PCR A, only 21.4% of the COVID-19 patients would be considered positive. The accuracy of all methods reached nearly 100% when saliva and NPS samples from the same patient were tested simultaneously.ConclusionsSARS-CoV-2 nucleic acid detection methods should be fully evaluated before use. High-positivity rate methods such as RT-RAA and dd-RT-PCR should be considered when possible. Furthermore, saliva after deep cough and NPS can greatly improve the accuracy of the diagnosis, and testing OPS alone is not recommended.

scholarly journals Analytical Ancestry: “Firsts” in Fluorescent Labeling of Nucleosides, Nucleotides, and Nucleic Acids

2009 ◽  
Vol 55 (4) ◽  
pp. 670-683 ◽  
Author(s):  
Larry J Kricka ◽  
Paolo Fortina
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Fluorescent Dyes ◽  
Fluorescent Labeling ◽  
Covalent Attachment ◽  
Detection Methods ◽  
Fluorescent Label ◽  
Nucleic Acid Detection ◽  
Fluorescent Labels ◽  
Fluorescent Properties

Abstract Background: The inherent fluorescent properties of nucleosides, nucleotides, and nucleic acids are limited, and thus the need has arisen for fluorescent labeling of these molecules for a variety of analytical applications. Content: This review traces the analytical ancestry of fluorescent labeling of nucleosides, nucleotides, and nucleic acids, with an emphasis on the first to publish or patent. The scope of labeling includes (a) direct labeling by covalent labeling of nucleic acids with a fluorescent label or noncovalent binding or intercalation of a fluorescent dye to nucleic acids and (b) indirect labeling via covalent attachment of a secondary label to a nucleic acid, and then binding this to a fluorescently labeled ligand binder. An alternative indirect strategy involves binding of a nucleic acid to a nucleic acid binder molecule (e.g., antibody, antibiotic, histone, antibody, nuclease) that is labeled with a fluorophore. Fluorescent labels for nucleic acids include organic fluorescent dyes, metal chelates, carbon nanotubes, quantum dots, gold particles, and fluorescent minerals. Summary: Fluorescently labeled nucleosides, nucleotides, and nucleic acids are important types of reagents for biological assay methods and underpin current methods of chromosome analysis, gel staining, DNA sequencing and quantitative PCR. Although these methods use predominantly organic fluorophores, new types of particulate fluorophores in the form of nanoparticles, nanorods, and nanotubes may provide the basis of a new generation of fluorescent labels and nucleic acid detection methods.

scholarly journals Genomic Surveillance Enables Suitability Assessment of Salmonella Gene Targets Used for Culture-Independent Diagnostic Testing

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Rebecca J. Rockett ◽  
Alicia Arnott ◽  
Qinning Wang ◽  
Peter Howard ◽  
Vitali Sintchenko
Keyword(s):  
Diagnostic Testing ◽  
Laboratory Diagnosis ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Diagnostic Systems ◽  
Gene Target ◽  
Single Nucleotide ◽  
Suitability Assessment ◽  
Culture Independent ◽  
Conserved Gene

ABSTRACT Salmonella is a highly diverse genus consisting of over 2,600 serovars responsible for high-burden food- and waterborne gastroenteritis worldwide. Sensitivity and specificity of PCR-based culture-independent diagnostic testing (CIDT) systems for Salmonella, which depend on a highly conserved gene target, can be affected by single nucleotide polymorphisms (SNPs), indels, and genomic rearrangements within primer and probe sequences. This report demonstrates the value of prospectively collected genomic data for verifying CIDT targets. We utilized the genomes of 3,165 Salmonella isolates prospectively collected and sequenced in Australia. The sequences of Salmonella CIDT PCR gene targets (ttrA, spaO, and invA) were systematically interrogated to measure nucleotide dissimilarity. Analysis of 52 different serovars and 79 multilocus sequencing types (MLST) demonstrated dissimilarity within and between PCR gene targets ranging between 0 and 81.3 SNP/kbp (0 and 141 SNPs). The lowest average dissimilarity was observed in the ttrA target gene used by the Roche LightMix at 2.0 SNP/kbp (range, 0 to 46.7); however, entropy across the gene demonstrates that it may not be the most stable CIDT target. While debate continues over the benefits and pitfalls of replacing bacterial culture with molecular assays, the growing volumes of genomic surveillance data enable periodic regional reassessment and validation of CIDT targets against both prevalent and emerging serovars. If PCR systems are to become the primary screening and diagnostic tool for laboratory diagnosis of salmonellosis, ongoing monitoring of the genomic diversity in PCR target regions is warranted, as is the potential inclusion of two Salmonella PCR targets in frontline diagnostic systems.

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