scholarly journals CRISPR-Cas Systems for Diagnosing Infectious Diseases

2020 ◽  
Author(s):  
Anastasiya Kostyusheva ◽  
Sergey Brezgin ◽  
Yurii Babin ◽  
Irina Vasil'eva ◽  
Dmitry Kostyushev ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Molecular Diagnostics ◽  
Large Scale ◽  
Point Of Care ◽  
Disease Spread ◽  
Detection Methods ◽  
Epidemiological Surveillance ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Wide Range

Infectious diseases are a global health problem affecting billions of people. Developing rapid and sensitive diagnostic tools is key for successful patient management and curbing disease spread. Currently available diagnostics are very specific and sensitive but time-consuming and require expensive laboratory settings and well-trained personnel; thus, they are not available in resource-limited areas, for the purposes of large-scale screenings and in case of outbreaks and epidemics. Developing new, rapid, and affordable point-of-care diagnostic assays is urgently needed. This review focuses on CRISPR-based technologies and their perspectives to become platforms for point-of-care nucleic acid detection methods and as deployable diagnostic platforms that could help to identify and curb outbreaks and emerging epidemics. We describe the mechanisms and function of different classes and types of CRISPR-Cas systems, including pros and cons for developing molecular diagnostic tests and applications of each type to detect a wide range of infectious agents. Many Cas proteins (Cas9, Cas12, Cas13, Cas14) have been leveraged to create highly accurate and sensitive diagnostic tools combined with technologies of signal amplification and fluorescent, potentiometric, colorimetric, or lateral flow assay detection. In particular, the most advanced platforms -- SHERLOCK/v2, DETECTR, or CRISPR-Chip -- enable detection of attomolar amounts of pathogenic nucleic acids with specificity comparable to that of PCR but with minimal technical settings. Further developing CRISPR-based diagnostic tools promises to dramatically transform molecular diagnostics, making them easily affordable and accessible virtually anywhere in the world. The burden of socially significant diseases, frequent outbreaks, recent epidemics (MERS, SARS and the ongoing coronoviral nCov-2019 infection) urgently need the developing of express-diagnostic tools. Recently devised CRISPR-technologies represent the unprecedented opportunity to reshape epidemiological surveillance and molecular diagnostics.

scholarly journals Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection

2021 ◽  
Vol 34 (3) ◽  
Author(s):  
Seyed Hamid Safiabadi Tali ◽  
Jason J. LeBlanc ◽  
Zubi Sadiq ◽  
Oyejide Damilola Oyewunmi ◽  
Carolina Camargo ◽  
...  
Keyword(s):  
Large Scale ◽  
Imaging Techniques ◽  
Point Of Care ◽  
Lessons Learned ◽  
Disease Spread ◽  
Infection Prevention And Control ◽  
Diagnostic Tools ◽  
Specimen Collection ◽  
Recent Developments ◽  
And Control

SUMMARY The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.

scholarly journals Recent Developments towards Portable Point-of-Care Diagnostic Devices for Pathogen Detection

2022 ◽  
Author(s):  
Sharmili Roy ◽  
FAREEHA ARSHAD ◽  
Shimaa Eissa ◽  
Mohammadali Safavieh ◽  
Sanaa G. Alattas ◽  
...  
Keyword(s):  
Global Health ◽  
Infectious Diseases ◽  
Pathogen Detection ◽  
Point Of Care ◽  
Rapid Development ◽  
Diagnostic Tools ◽  
Recent Developments

The rapid development of accurate and quick diagnostic tools for infectious diseases has made a massive impact in global health. POC devices for pathogen detection have primarily contributed to clinical...

scholarly journals Testing Denmark: A Danish nationwide surveillance study of COVID-19

2021 ◽  
Author(s):  
Kamille Fogh ◽  
Jarl E Strange ◽  
Bibi FSS Scharff ◽  
Alexandra RR Eriksen ◽  
Rasmus B Hasselbalch ◽  
...  
Keyword(s):  
Large Scale ◽  
Point Of Care ◽  
Rapid Test ◽  
Physical Contact ◽  
Surveillance Study ◽  
Epidemiological Surveillance ◽  
Danish Population ◽  
Positive Polymerase Chain Reaction ◽  
Geographic Population ◽  
Associated Risk Factors

Background National data on the spread of SARS-CoV-2 infection and knowledge on associated risk factors are important for understanding the course of the pandemic. Testing Denmark is a national large-scale epidemiological surveillance study of SARS-CoV-2 in the Danish population. Methods Between September and October 2020, approximately 1.3 million of 5.8 million Danish citizens (age > 15 years) were randomly invited to fill in an electronic questionnaire covering COVID-19 exposures and symptoms. The prevalence of SARS-CoV-2 antibodies was determined by Point-of Care rapid Test (POCT) distributed to participants home addresses. Findings In total 318,552 participants (24.5% invitees) completed the questionnaire and provided the result of the POCT. Of these, 2,519 (0.79%) were seropositive (median age 55 years) and women were more often seropositive than men, interquartile range (IQR) 42-64, 40.2% males. Of participants with a prior positive Polymerase Chain Reaction (PCR) test (n=1,828), 29.1% were seropositive in the POCT. Seropositivity increased with age irrespective of sex. Elderly participants (>61 years) reported less symptoms and had less frequently been tested for SARS-CoV-2 compared to younger participants. Seropositivity was associated with physical contact with SARS-CoV-2 infected individuals (Risk ratio (RR) 7.43, 95% CI: 6.57-8.41) and in particular household members (RR 17.70, 95% CI: 15.60-20.10). Home care workers had a higher risk of seropositivity (RR 2.09 (95% CI: 1.58-2.78) as compared to office workers. Geographic population density was not associated to seropositivity. A high degree of compliance with national preventive recommendations was reported (e.g., > 80% use of face masks), but no difference was found between seropositive and seronegative participants. Interpretation This study provides insight into the immunity of the Danish population seven to eight months after the first COVID-19 case in Denmark. The seroprevalence was lower than expected probably due to a low sensitivity of the POCT used or due to challenges relating to the reading of test results. Occupation or exposure in local communities were major routes of infection. As elderly participants were more often seropositive despite fewer symptoms and less PCR tests performed, more emphasis should be placed on testing this age group.

scholarly journals Are Staphylococcus intermedius Infections in Humans Cases of Mistaken Identity? A Case Series and Literature Review

2015 ◽  
Vol 2 (3) ◽  
Author(s):  
Roberto Viau ◽  
Andrea M. Hujer ◽  
Kristine M. Hujer ◽  
Robert A. Bonomo ◽  
Robin L.P. Jump
Keyword(s):  
Literature Review ◽  
Molecular Diagnostics ◽  
Case Series ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Human Pathogen ◽  
Detailed Review ◽  
Mistaken Identity ◽  
Staphylococcus Intermedius ◽  
Microbiological Methods

Abstract Staphylococcus intermedius and Staphylococcus pseudintermedius are difficult to distinguish using conventional microbiological methods. Molecular diagnostic tools change our understanding of the epidemiology of these 2 organisms. In this study, we present (1) a detailed review of the current literature on molecular diagnostics and (2) a case series in which misidentification was proven in 1 case. We conclude that S pseudintermedius is a more common human pathogen than previously recognized.

scholarly journals A Lab-on-a-Chip Device Integrated DNA Extraction and Solid Phase PCR Array for the Genotyping of High-Risk HPV in Clinical Samples

Micromachines ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 537 ◽  
Author(s):  
Cancan Zhu ◽  
Anzhong Hu ◽  
Junsheng Cui ◽  
Ke Yang ◽  
Xinchao Zhu ◽  
...  
Keyword(s):  
High Risk ◽  
Dna Extraction ◽  
Molecular Diagnostics ◽  
Solid Phase ◽  
Lab On A Chip ◽  
Clinical Diagnostics ◽  
Oligonucleotide Array ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Multiplex Amplification

Point-of-care (POC) molecular diagnostics play a crucial role in the prevention and treatment of infectious diseases. It is necessary to develop portable, easy-to-use, inexpensive and rapid molecular diagnostic tools. In this study, we proposed a lab-on-a-chip device that integrated DNA extraction, solid-phase PCR and genotyping detection. The ingenious design of the pneumatic microvalves enabled the fluid mixing and reagent storage to be organically combined, significantly reducing the size of the chip. The solid oligonucleotide array incorporated into the chip allowed the spatial separation of the primers and minimized undesirable interactions in multiplex amplification. As a proof-of-concept for POC molecular diagnostics on the device, five genotypes of high-risk human papillomavirus (HPV) (HPV16/HPV18/HPV31/HPV33/HPV58) were examined. Positive quality control samples and HPV patient cervical swab specimens were analyzed on the integrated microdevice. The platform was capable of detection approximately 50 copies of HPV virus per reaction during a single step, including DNA extraction, solid-phase PCR and genotype detection, in 1 h from samples being added to the chip. This simple and inexpensive microdevice provided great utility for the screening and monitoring of HPV genotypes. The sample-to-result platform will pave the way for wider application of POC molecular testing in the fields of clinical diagnostics, food safety, and environmental monitoring.

scholarly journals Point-of-Care Diagnostic Tools for Surveillance of SARS-CoV-2 Infections

2021 ◽  
Vol 9 ◽  
Author(s):  
Dhanasekaran Sakthivel ◽  
David Delgado-Diaz ◽  
Laura McArthur ◽  
William Hopper ◽  
Jack S. Richards ◽  
...  
Keyword(s):  
Large Scale ◽  
Clinical Symptoms ◽  
Point Of Care ◽  
Cost Effective ◽  
Nucleic Acid Amplification ◽  
Diagnostic Tools ◽  
Rt Pcr ◽  
Serological Tests ◽  
Polymerase Chain ◽  
Effective Public Health

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a recently emerged and highly contagious virus that causes coronavirus disease 2019 (COVID-19). As of August 24, 2021, there were more than 212 million confirmed COVID-19 cases and nearly 4.4 million deaths reported globally. Early diagnosis and isolation of infected individuals remains one of the most effective public health interventions to control SARS-CoV-2 spread and for effective clinical management of COVID-19 cases. Currently, SARS-CoV-2 infection is diagnosed presumptively based on clinical symptoms and confirmed by detecting the viral RNA in respiratory samples using reverse transcription polymerase chain reaction (RT-PCR). Standard RT-PCR protocols are time consuming, expensive, and technically demanding, which makes them a poor choice for large scale and point-of-care screening in resource-poor settings. Recently developed isothermal nucleic acid amplification tests (iNAAT), antigen and/or serological tests are cost-effective to scale COVID-19 testing at the point-of-care (PoC) and for surveillance activities. This review discusses the development of rapid PoC molecular tools for the detection and surveillance of SARS-CoV-2 infections.

scholarly journals Intensivists’ beliefs about rapid multiplex molecular diagnostic testing and its potential role in improving prescribing decisions and antimicrobial stewardship: a qualitative study

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Alyssa M. Pandolfo ◽  
Robert Horne ◽  
Yogini Jani ◽  
Tom W. Reader ◽  
Natalie Bidad ◽  
...  
Keyword(s):  
Molecular Diagnostics ◽  
Antimicrobial Stewardship ◽  
Diagnostic Tests ◽  
Pathogenic Bacteria ◽  
Point Of Care ◽  
Diagnostic Testing ◽  
Molecular Diagnostic ◽  
Antibiotic Prescribing ◽  
Test Results ◽  
Structured Interviews

Abstract Background Rapid molecular diagnostic tests to investigate the microbial aetiology of pneumonias may improve treatment and antimicrobial stewardship in intensive care units (ICUs). Clinicians’ endorsement and uptake of these tests is crucial to maximise engagement; however, adoption may be impeded if users harbour unaddressed concerns or if device usage is incompatible with local practice. Accordingly, we strove to identify ICU clinicians’ beliefs about molecular diagnostic tests for pneumonias before implementation at the point-of-care. Methods We conducted semi-structured interviews with 35 critical care doctors working in four ICUs in the United Kingdom. A clinical vignette depicting a fictitious patient with signs of pneumonia was used to explore clinicians’ beliefs about the importance of molecular diagnostics and their concerns. Data were analysed thematically. Results Clinicians’ beliefs about molecular tests could be grouped into two categories: perceived potential of molecular diagnostics to improve antibiotic prescribing (Molecular Diagnostic Necessity) and concerns about how the test results could be implemented into practice (Molecular Diagnostic Concerns). Molecular Diagnostic Necessity stemmed from beliefs that positive results would facilitate targeted antimicrobial therapy; that negative results would signal the absence of a pathogen, and consequently that having the molecular diagnostic results would bolster clinicians’ prescribing confidence. Molecular Diagnostic Concerns included unfamiliarity with the device’s capabilities, worry that it would detect non-pathogenic bacteria, uncertainty whether it would fail to detect pathogens, and discomfort with withholding antibiotics until receiving molecular test results. Conclusions Clinicians believed rapid molecular diagnostics for pneumonias were potentially important and were open to using them; however, they harboured concerns about the tests’ capabilities and integration into clinical practice. Implementation strategies should bolster users’ necessity beliefs while reducing their concerns; this can be accomplished by publicising the tests’ purpose and benefits, identifying and addressing clinicians’ misconceptions, establishing a trial period for first-hand familiarisation, and emphasising that, with a swift (e.g., 60–90 min) test, antibiotics can be started and refined after molecular diagnostic results become available.

scholarly journals A diagnostic multiplex PCR scheme for identification of plant-associated bacteria of the genusPantoea

2018 ◽  
Author(s):  
Kossi Kini ◽  
Raoul Agnimonhan ◽  
Rachelle Dossa ◽  
Drissa Silué ◽  
Ralf Koebnik
Keyword(s):  
Multiplex Pcr ◽  
Plant Protection ◽  
Detection Threshold ◽  
Leaf Blight ◽  
Crop Plants ◽  
Plant Diseases ◽  
Bacterial Leaf Blight ◽  
Epidemiological Surveillance ◽  
Molecular Diagnostic ◽  
Diagnostic Tools

AbstractBackgroundThe genusPantoeaforms a complex of more than 25 species, among which several cause diseases of several crop plants, including rice. Notably, strains ofPantoea ananatisandPantoea stewartiihave been found to cause bacterial leaf blight of rice in Togo and Benin, while other authors have observed thatPantoea agglomeranscan also cause bacterial leaf blight of rice. The contribution of these and perhaps other species ofPantoeato plant diseases and yield losses of crop plants is currently not well documented, partly due to the lack of efficient diagnostic tools.ResultUsing 34 whole genome sequences of the three-major plant-pathogenicPantoeaspecies, a set of PCR primers that specifically detect each of the three species,P. agglomerans,P. ananatis, andP. stewartii, was designed. A multiplex PCR protocol which can distinguish these three species and also detects members of otherPantoeaspecies was further developed. Upon validation on a set of reference strains, 609 suspectedPantoeastrains that were isolated from rice leaves or seeds originating from 11 African countries were screened. In total, 41P. agglomeransstrains from eight countries, 79P. ananatisstrains from nine countries, 269P. stewartiistrains from nine countries and 220 unsolvedPantoeastrains from ten countries were identified. The PCR protocol allowed detectingPantoeabacteria grown in vitro, in planta and in rice seeds. The detection threshold was estimated at 5 ng/mL of total genomic DNA and 1 × 105CFU/mL of heated cells.ConclusionThis new molecular diagnostic tool will help accurately diagnose major plant-pathogenic species ofPantoea. Due to its robustness, specificity, sensitivity, and cost efficiency it will be very useful for plant protection services and for the epidemiological surveillance of these important crop-threatening bacteria.

A Microfluidic Approach and Enhancement Towards a Colorimetric Enzyme-Linked-Immunosorbant-Assay for Diagnostic Detection of Infectious Diseases

2007 ◽  
Author(s):  
Uland Liao ◽  
Armando Tovar ◽  
Philip Felgner ◽  
Abraham P. Lee
Keyword(s):  
Infectious Diseases ◽  
Detection Sensitivity ◽  
Detection Methods ◽  
Antibody Detection ◽  
Diagnostic Tools ◽  
Immunosorbant Assay ◽  
Children And Young Adults ◽  
Polymerase Chain ◽  
Enzyme Linked Immunosorbant Assay ◽  
Diagnostic Detection

Accounting for more than 13 million deaths a year, infectious diseases have become the world’s biggest killer of children and young adults worldwide [1]. Diagnostic tools and technologies are vital towards identifying the presence and treatment of these diseases. Detection methods have commonly relied on DNA using polymerase-chain-reaction (PCR), however antibody methods have become popular due to growing trends in technology and detection sensitivity. ImmPORT Therapeutics, a leading group in generating infectious disease proteome microarrays, has developed multiplex systems for comprehensive analysis of immune responses to multiple infectious diseases [2]. Current microarray handling however requires conventional lab-bench methods that require whole-day processes and large amounts of user-handling confined to laboratory settings. Miniaturization of laboratory processes would provide numerous advantages in terms of cost, time, portability and multistage automation in addition to what is already offered. The proposed microfluidic device is a colorimetric enzyme-linked-immunosorbant assay (ELISA) for antibody detection of infectious agents that draws on ImmPORT Therapeutics technology with a purpose of decreasing reagent volumes and times potentially unattainable through conventional methods.

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