scholarly journals Combined use of metagenomic sequencing and host response profiling for the diagnosis of suspected sepsis

2019 ◽  
Author(s):  
Henry K. Cheng ◽  
Susanna K. Tan ◽  
Timothy E. Sweeney ◽  
Pratheepa Jeganathan ◽  
Thomas Briese ◽  
...  
Keyword(s):  
Host Response ◽  
Diagnostic Techniques ◽  
Shotgun Sequencing ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Metagenomic Sequencing ◽  
Suspected Sepsis ◽  
Bacterial Dna ◽  
Dna 2 ◽  
Capture Sequencing

ABSTRACTBackgroundCurrent diagnostic techniques are inadequate for rapid microbial diagnosis and optimal management of patients with suspected sepsis. We assessed the clinical impact of three powerful molecular diagnostic methods.MethodsWith blood samples from 200 consecutive patients with suspected sepsis, we evaluated 1) metagenomic shotgun sequencing together with a Bayesian inference approach for contaminant sequence removal, for detecting bacterial DNA; 2) viral capture sequencing; and 3) transcript-based host response profiling for classifying patients as infected or not, and if infected, with bacteria or viruses. We then evaluated changes in diagnostic decision-making among three expert physicians by unblinding the results of these methods in a staged fashion.ResultsMetagenomic shotgun sequencing confirmed positive blood culture results in 14 of 26 patients. In 17 of 200 patients, metagenomic sequencing and viral capture sequencing revealed organisms that were 1) not detected by conventional hospital tests within 5 days after presentation, and 2) classified as of probable clinical relevance by physician consensus. Host response profiling led at least two of three physicians to change their diagnostic decisions in 46 of 100 patients. The data suggested possible bacterial DNA translocation in 8 patients who were originally classified by physicians as noninfected and illustrate how host response profiling can guide interpretation of metagenomic shotgun sequencing results.ConclusionsThe integration of host response profiling, metagenomic shotgun sequencing, and viral capture sequencing enhances the utility of each, and may improve the diagnosis and management of patients with suspected sepsis.

scholarly journals A Recent Update on Advanced Molecular Diagnostic Techniques for COVID-19 Pandemic: An Overview

2021 ◽  
Vol 12 ◽  
Author(s):  
Akanksha Roberts ◽  
Raghuraj Singh Chouhan ◽  
Deepshikha Shahdeo ◽  
Narlawar Sagar Shrikrishna ◽  
Veerbhan Kesarwani ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Electrochemical Sensors ◽  
Cost Effective ◽  
Surface Enhanced Raman Spectroscopy ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques ◽  
Rt Pcr ◽  
Ongoing Research

Coronavirus disease 2019 (COVID-19), which started out as an outbreak of pneumonia, has now turned into a pandemic due to its rapid transmission. Besides developing a vaccine, rapid, accurate, and cost-effective diagnosis is essential for monitoring and combating the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its related variants on time with precision and accuracy. Currently, the gold standard for detection of SARS-CoV-2 is Reverse Transcription Polymerase Chain Reaction (RT-PCR), but it lacks accuracy, is time-consuming and cumbersome, and fails to detect multi-variant forms of the virus. Herein, we have summarized conventional diagnostic methods such as Chest-CT (Computed Tomography), RT-PCR, Loop Mediated Isothermal Amplification (LAMP), Reverse Transcription-LAMP (RT-LAMP), as well new modern diagnostics such as CRISPR–Cas-based assays, Surface Enhanced Raman Spectroscopy (SERS), Lateral Flow Assays (LFA), Graphene-Field Effect Transistor (GraFET), electrochemical sensors, immunosensors, antisense oligonucleotides (ASOs)-based assays, and microarrays for SARS-CoV-2 detection. This review will also provide an insight into an ongoing research and the possibility of developing more economical tools to tackle the COVID-19 pandemic.

scholarly journals Advanced CRISPR-Cas Effector Enzyme-Based Diagnostics for Infectious Diseases, Including COVID-19

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1356
Author(s):  
Sangha Kwon ◽  
Ha Youn Shin
Keyword(s):  
Nucleic Acid ◽  
Infectious Diseases ◽  
Pathogen Detection ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Nucleic Acid Amplification ◽  
Detection Methods ◽  
Molecular Diagnostic ◽  
Nucleic Acid Detection ◽  
Time Accuracy

Rapid and precise diagnostic tests can prevent the spread of diseases, including worldwide pandemics. Current commonly used diagnostic methods include nucleic-acid-amplification-based detection methods and immunoassays. These techniques, however, have several drawbacks in diagnosis time, accuracy, and cost. Nucleic acid amplification methods are sensitive but time-consuming, whereas immunoassays are more rapid but relatively insensitive. Recently developed CRISPR-based nucleic acid detection methods have been found to compensate for these limitations. In particular, the unique collateral enzymatic activities of Cas12 and Cas13 have dramatically reduced the diagnosis times and costs, while improving diagnostic accuracy and sensitivity. This review provides a comprehensive description of the distinct enzymatic features of Cas12 and Cas13 and their applications in the development of molecular diagnostic platforms for pathogen detection. Moreover, it describes the current utilization of CRISPR-Cas-based diagnostic techniques to identify SARS-CoV-2 infection, as well as recent progress in the development of CRISPR-Cas-based detection strategies for various infectious diseases. These findings provide insights into designing effective molecular diagnostic platforms for potential pandemics.

scholarly journals DNA-Detection Based Diagnostics for Taenia solium Cysticercosis in Porcine

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Maxwell W. Waema ◽  
Gerald Misinzo ◽  
John M. Kagira ◽  
Eric L. Agola ◽  
Helena A. Ngowi
Keyword(s):  
Diagnostic Tool ◽  
Dna Detection ◽  
Taenia Solium ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Intermediate Hosts ◽  
Low Resource ◽  
Porcine Cysticercosis

Porcine cysticercosis is a neglected and underestimated disease caused by metacestode stage of the tapeworm, Taenia solium (T. solium). Pigs are the intermediate hosts of T. solium while human are the only known definitive host. The disease has an economic consequence because the affected farmers lose 50−100 percent of the value of pigs if they are infected. Lack of affordable, easy to use, sensitive, and specific molecular diagnostic tools for detection of infections at the farm level hinders the control of porcine cysticercosis in endemic areas. A number of DNA based diagnostic assays for the detection of T. solium infections in pigs have been developed and evaluated but none is applicable at low-resource areas where this disease is an endemic. This review focuses mainly on DNA based diagnostic methods, their sensitivity, specificity, and utilization at low-resource areas. We summarized data from 65 studies on the current DNA-detection based diagnostic techniques for T. solium cysticercosis in porcine, published in English between the years 2000–2018, identified through PubMed search engine. Of the different polymerase chain reaction (PCR) assays developed for identification of T. solium, the most sensitive (97−100%) and specific (100%) one is nested PCR. One study utilized loop-mediated isothermal amplification (LAMP) as a diagnostic tool for the detection of T. solium infections though its field use was never determined. Recombinase polymerase amplification (RPA) has been evaluated as a diagnostic tool for a variety of diseases, but has never been exploited for the diagnosis of cysticercosis/taeniasis. In conclusion, several molecular methods have been developed and evaluated in lab settings. However, there is need to validate these methods as a diagnostic tool to diagnose porcine cysticercosis in low-resource areas.

scholarly journals Propylene Glycol and Non-Destructive DNA Extractions Enable Preservation and Isolation of Insect and Hosted Bacterial DNA

Agriculture ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 77
Author(s):  
Francesco Martoni ◽  
Elisse Nogarotto ◽  
Alexander M. Piper ◽  
Rachel Mann ◽  
Isabel Valenzuela ◽  
...  
Keyword(s):  
Propylene Glycol ◽  
Extraction Methods ◽  
Diagnostic Techniques ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques ◽  
Multiple Time ◽  
Agricultural Pests ◽  
Bacterial Dna ◽  
Dna Preservation ◽  
Non Destructive

Plant bio-protection and biosecurity programs worldwide use trap-based surveillance for the early detection of agricultural pests and pathogens to contain their incursions and spread. This task is reliant on effective preservation in insect traps, which is required to maintain specimen quality for extended periods under variable environmental conditions. Furthermore, with traditional morphological examinations now increasingly paired with modern molecular diagnostic techniques, insect traps are required to preserve both the specimens’ morphology and the DNA of insects and vectored bacterial pathogens. Here, we used psyllids (Hemiptera) and their hosted bacteria as a model to test the preservative ability of propylene glycol (PG): a non-flammable, easily transportable preservative agent that could be used in pitfall, suction or malaise traps. We tested preservation using various PG concentrations, at different temperatures and for multiple time periods, paired with non-destructive DNA extraction methods, which allow isolation of both insect and arbobacterial DNA while retaining a morphological voucher of the insect host specimens. PG concentrations between 40% and 100% performed best for both insect and bacterial DNA preservation up to 28 days. Ultimately, given the viscous nature of PG at high concentrations, we recommend using it at a concentration between 40% and 60% to enable insects to sink into the solution, thus enhancing DNA preservation.

scholarly journals Molecular and Immunological Diagnostic Techniques of Medical Viruses

2020 ◽  
Vol 2020 ◽  
pp. 1-19
Author(s):  
Daniel Hussien Reta ◽  
Tesfaye Sisay Tessema ◽  
Addis Simachew Ashenef ◽  
Adey Feleke Desta ◽  
Wajana Lako Labisso ◽  
...  
Keyword(s):  
Low Income ◽  
Viral Infections ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Low Income Countries ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Molecular Diagnostic Techniques ◽  
Global Public Health ◽  
Patient Sample

Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.

scholarly journals RT-LAMP CRISPR-Cas12/13-Based SARS-CoV-2 Detection Methods

Diagnostics ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1646
Author(s):  
Kasturi Selvam ◽  
Mohamad Ahmad Najib ◽  
Muhammad Fazli Khalid ◽  
Suharni Mohamad ◽  
Fahreddin Palaz ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Quantitative Polymerase Chain Reaction ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Molecular Diagnostic ◽  
Public Attention ◽  
Laboratory Equipment ◽  
Highly Sensitive ◽  
Polymerase Chain

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription–quantitative polymerase chain reaction (RT-qPCR). However, RT-qPCR can only be performed in centralized laboratories due to the requirement for advanced laboratory equipment and qualified workers. In the last decade, clustered regularly interspaced short palindromic repeats (CRISPR) technology has shown considerable promise in the development of rapid, highly sensitive, and specific molecular diagnostic methods that do not require complicated instrumentation. During the current COVID-19 pandemic, there has been growing interest in using CRISPR-based diagnostic techniques to develop rapid and accurate assays for detecting SARS-CoV-2. In this work, we review and summarize reverse-transcription loop-mediated isothermal amplification (RT-LAMP) CRISPR-based diagnostic techniques for detecting SARS-CoV-2.

Forensic research of staff fraud

2020 ◽  
Vol 23 (5) ◽  
pp. 585-600
Author(s):  
V.A. Timchenko
Keyword(s):  
Effective Means ◽  
Criminal Activity ◽  
Diagnostic Techniques ◽  
Scientific Basis ◽  
Diagnostic Methods ◽  
Structural Units ◽  
Forensic Research ◽  
Economic Information ◽  
Commercial Organizations ◽  
Original Approach

Subject. This article deals with the issues of forensic diagnostics, which is an effective means of detecting, preventing and suppressing staff fraud. Objectives. The article aims to present an original approach to the development of methods of forensic diagnosis of staff fraud based on the modeling method. It is also intended to identify a structure of staff fraud patterns and justify the need to classify the staff fraud methods. Methods. For the study, I used the methods of comparative analysis, systematization, induction, and deduction. Results. The article defines approaches to the formation of diagnostic methods of staff fraud and presents typical inconsistencies that arise in economic information under the influence of fraudulent actions of staff. It describes some diagnostic techniques that can detect staff fraud elements that occur in certain ways of criminal activity. Conclusions and Relevance. The proposed original approach helps develop standard and specific methods for diagnosing staff fraud on a scientific basis. The provisions outlined in the article can serve as a basis for scholarly discussion, contribute to the effectiveness of research on counter-fraud in the field of personnel fraud, and can be applied to the practical activities of structural units and individuals whose task is to combat staff fraud in commercial organizations.

scholarly journals Tick-borne zoonoses and commonly used diagnostic methods in human and veterinary medicine

2021 ◽  
Author(s):  
Andrea Springer ◽  
Antje Glass ◽  
Julia Probst ◽  
Christina Strube
Keyword(s):  
Veterinary Medicine ◽  
Diagnostic Tests ◽  
One Health ◽  
Animal Health ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Diagnostic Tools ◽  
Zoonotic Pathogens ◽  
Health Concept ◽  
The One

AbstractAround the world, human health and animal health are closely linked in terms of the One Health concept by ticks acting as vectors for zoonotic pathogens. Animals do not only maintain tick cycles but can either be clinically affected by the same tick-borne pathogens as humans and/or play a role as reservoirs or sentinel pathogen hosts. However, the relevance of different tick-borne diseases (TBDs) may vary in human vs. veterinary medicine, which is consequently reflected by the availability of human vs. veterinary diagnostic tests. Yet, as TBDs gain importance in both fields and rare zoonotic pathogens, such as Babesia spp., are increasingly identified as causes of human disease, a One Health approach regarding development of new diagnostic tools may lead to synergistic benefits. This review gives an overview on zoonotic protozoan, bacterial and viral tick-borne pathogens worldwide, discusses commonly used diagnostic techniques for TBDs, and compares commercial availability of diagnostic tests for humans vs. domestic animals, using Germany as an example, with the aim of highlighting existing gaps and opportunities for collaboration in a One Health framework.

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