scholarly journals Analytical and Clinical Assessment of a Portable, Isothermal Recombinase Polymerase Amplification (RPA) Assay for the Molecular Diagnosis of Urogenital Schistosomiasis

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4175
Author(s):  
John Archer ◽  
Rebecca Barksby ◽  
Tom Pennance ◽  
Penelope Rostron ◽  
Faki Bakar ◽  
...  

Accurate diagnosis of urogenital schistosomiasis is crucial for disease surveillance and control. Routine diagnostic methods, however, lack sensitivity when assessing patients with low levels of infection still able to maintain pathogen transmission. Therefore, there is a need for highly sensitive diagnostic tools that can be used at the point-of-care in endemic areas. Recombinase polymerase amplification (RPA) is a rapid and sensitive diagnostic tool that has been used to diagnose several pathogens at the point-of-care. Here, the analytical performance of a previously developed RPA assay (RT-ShDra1-RPA) targeting the Schistosoma haematobium Dra1 genomic region was assessed using commercially synthesised S. haematobium Dra1 copies and laboratory-prepared samples spiked with S. haematobium eggs. Clinical performance was also assessed by comparing diagnostic outcomes with that of a reference diagnostic standard, urine-egg microscopy. The RT-ShDra1-RPA was able to detect 1 × 101 copies of commercially synthesised Dra1 DNA as well as one S. haematobium egg within laboratory-spiked ddH2O samples. When compared with urine-egg microscopy, the overall sensitivity and specificity of the RT-ShDra1-RPA assay was 93.7% (±88.7–96.9) and 100% (±69.1–100), respectively. Positive and negative predictive values were 100% (±97.5–100) and 50% (±27.2–72.8), respectively. The RT-ShDra1-RPA therefore shows promise as a rapid and highly sensitive diagnostic tool able to diagnose urogenital schistosomiasis at the point-of-care.

2016 ◽  
Author(s):  
Bastian Kern ◽  
Patrick Jöckel

Abstract. Numerical climate and weather models have advanced to finer scales, accompanied by large amount of output data. The model systems hit the input and output (I/O) bottleneck of modern High Performance Computing (HPC) systems. We aim to apply diagnostic methods on-line during the model simulation instead of applying them as a post-processing step to written output data, to reduce the amount of I/O. To include diagnostic tools into the model system, we implemented a standardised, easy-to-use interface based on the Modular Earth Submodel System (MESSy) into the ICOsahedral Non-hydrostatic (ICON) modelling framework. The integration of the diagnostic interface into the model system is briefly described. Furthermore, we present a prototype implementation of an advanced on-line diagnostic tool for the aggregation of model data onto a user-defined regular coarse grid. This diagnostic tool will be used to reduce the amount of model output in future simulations. Performance tests of the interface and of two different diagnostic tools show, that the interface itself introduces no overhead in form of additional runtime to the model system. The diagnostic tools, however, have significant impact on the model system's runtime. This overhead strongly depends on the characteristics and implementation of the diagnostic tool. The diagnostic tool with high inter-process communication introduces large overhead, whereas the additional runtime of the diagnostic tool without inter-process communication is low. We briefly describe our efforts to reduce the additional runtime from the diagnostic tools, and present a brief analysis of memory consumption. Future work will focus on optimisation of the memory footprint and the I/O operations of the diagnostic interface.


2021 ◽  
Vol 4 ◽  
pp. 28
Author(s):  
Farisai Chidzwondo ◽  
Francisca Mutapi

Frequent disease outbreaks and acute infections occur in rural and low-income urban areas of Africa, with many health systems unprepared to diagnose and control diseases that are recurrent, endemic or have extended their geographic zone. In this review, we focus on acute infections that can be characterized by sudden onset, rapid progression, severe symptoms and poor prognosis. Consequently, these infections require early diagnosis and intervention. While effective vaccines have been developed against some of these diseases, lack of compliance and accessibility, and the need for repeated or multiple vaccinations mean large populations can remain vulnerable to infection. It follows that there is a need for enhancement of national surveillance and diagnostic capacity to avert morbidity and mortality from acute infections. We discuss the limitations of traditional diagnostic methods and explore the relative merits and applicability of protein-, carbohydrate- and nucleic acid-based rapid diagnostic tests that have been trialled for some infectious diseases. We also discuss the utility and limitations of antibody-based serological diagnostics and explore how systems biology approaches can better inform diagnosis. Lastly, given the complexity and high cost associated with after-service support of emerging technologies, we propose that, for resource-limited settings in Africa, multiplex point-of-care diagnostic tools be tailor-made to detect both recurrent acute infections and endemic infections.


2019 ◽  
Vol 58 (1) ◽  
pp. 138-145 ◽  
Author(s):  
Federica Braga ◽  
Elena Aloisio ◽  
Andrea Panzeri ◽  
Takahito Nakagawa ◽  
Mauro Panteghini

Abstract Background Highly sensitive cardiac troponin assays (hs-cTn) are not available as point-of-care (POC) measurements. As rapid testing cannot be achieved at the expense of clinical performance, there is an urgent need to develop and rigorously validate POC hs-cTn. Konica Minolta (KM) has recently developed a surface plasmon-field enhanced fluorescence spectroscopy-based POC hs-cTn I system. Methods We validated the analytical characteristics of the KM POC system according to the international guidelines. Results Limit of blank (LoB) and limit of detection (LoD) were 0.35 and 0.62 ng/L, respectively, hs-cTn I concentrations corresponding to a total CV of 20%, 10% and 5% were 1.5, 3.9 and 11.0 ng/L, respectively. Method comparison studies showed that KM calibration was successfully traced to higher-order references. Limit of quantitation (LoQ), i.e. the hs-cTn I concentration having a total error of measurement of ≤34%, was 10.0 ng/L. The upper reference limit (URL) for 600 healthy blood donors was calculated at 12.2 ng/L (90% confidence interval [CI]: 9.2–39.2), while sex-partitioned URLs were 20.6 (males) and 10.7 ng/L (females), respectively (p < 0.0001). KM assay measured hs-cTn I concentrations >LoD in 65.7% of all reference individuals, in 76.7% of males and in 54.7% of females, respectively. Conclusions The KM system joins the characteristics of POC systems to the analytical performance of hs-cTn.


2019 ◽  
Vol 5 (4) ◽  
pp. 90 ◽  
Author(s):  
Amir Arastehfar ◽  
Brian L. Wickes ◽  
Macit Ilkit ◽  
David H. Pincus ◽  
Farnaz Daneshnia ◽  
...  

Extensive advances in technology offer a vast variety of diagnostic methods that save time and costs, but identification of fungal species causing human infections remains challenging in developing countries. Since the echinocandins, antifungals widely used to treat invasive mycoses, are still unavailable in developing countries where a considerable number of problematic fungal species are present, rapid and reliable identification is of paramount importance. Unaffordability, large footprints, lack of skilled personnel, and high costs associated with maintenance and infrastructure are the main factors precluding the establishment of high-precision technologies that can replace inexpensive yet time-consuming and inaccurate phenotypic methods. In addition, point-of-care lateral flow assay tests are available for the diagnosis of Aspergillus and Cryptococcus and are highly relevant for developing countries. An Aspergillus galactomannan lateral flow assay is also now available. Real-time PCR remains difficult to standardize and is not widespread in countries with limited resources. Isothermal and conventional PCR-based amplification assays may be alternative solutions. The combination of real-time PCR and serological assays can significantly increase diagnostic efficiency. However, this approach is too expensive for medical institutions in developing countries. Further advances in next-generation sequencing and other innovative technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic tools may lead to efficient, alternate methods that can be used in point-of-care assays, which may supplement or replace some of the current technologies and improve the diagnostics of fungal infections in developing countries.


2016 ◽  
Vol 9 (10) ◽  
pp. 3639-3654
Author(s):  
Bastian Kern ◽  
Patrick Jöckel

Abstract. Numerical climate and weather models have advanced to finer scales, accompanied by large amounts of output data. The model systems hit the input and output (I/O) bottleneck of modern high-performance computing (HPC) systems. We aim to apply diagnostic methods online during the model simulation instead of applying them as a post-processing step to written output data, to reduce the amount of I/O. To include diagnostic tools into the model system, we implemented a standardised, easy-to-use interface based on the Modular Earth Submodel System (MESSy) into the ICOsahedral Non-hydrostatic (ICON) modelling framework. The integration of the diagnostic interface into the model system is briefly described. Furthermore, we present a prototype implementation of an advanced online diagnostic tool for the aggregation of model data onto a user-defined regular coarse grid. This diagnostic tool will be used to reduce the amount of model output in future simulations. Performance tests of the interface and of two different diagnostic tools show, that the interface itself introduces no overhead in form of additional runtime to the model system. The diagnostic tools, however, have significant impact on the model system's runtime. This overhead strongly depends on the characteristics and implementation of the diagnostic tool. A diagnostic tool with high inter-process communication introduces large overhead, whereas the additional runtime of a diagnostic tool without inter-process communication is low. We briefly describe our efforts to reduce the additional runtime from the diagnostic tools, and present a brief analysis of memory consumption. Future work will focus on optimisation of the memory footprint and the I/O operations of the diagnostic interface.


Parasitology ◽  
2014 ◽  
Vol 141 (14) ◽  
pp. 1912-1917 ◽  
Author(s):  
MARIA P. REBOLLO ◽  
MOSES JOHN BOCKARIE

SUMMARYLymphatic filariasis (LF), which is highly endemic in 73 countries worldwide, is targeted for elimination by 2020. The strategy for achieving this goal is based on 4 sequential programmatic steps: mapping, Mass drug administration (MDA) implementation, post-MDA surveillance and verification of LF elimination. All 4 stages of the implementation process are dependent on the availability of user friendly and highly sensitive rapid diagnostic tools. By the end of 2012, 59 countries had completed mapping for LF and Eritrea was the only country yet to start the process. Rolling out new diagnostic tools to facilitate the mapping process will enable an accelerated shrinking of the LF map to zero endemic countries by 2020. When the Global Programme to Eliminate Lymphatic Filariasis was launched in 2000, diagnostic tools for LF were limited to clinical examination, detection of microfilaria (MF) by microscopy in night blood samples and detection of antibodies to native-antigen preparations. There has been a significant improvement in the traditional LF diagnostic methods in recent years and some new tools are now available. This paper provides an update on the human diagnostic tests available for LF and their current applications as tools in mapping and transmission monitoring. The values of entomological indicators and parasite detection and speciation methods applied to vector populations are also discussed.


Materials ◽  
2021 ◽  
Vol 14 (24) ◽  
pp. 7851
Author(s):  
Koena L. Moabelo ◽  
Darius R. Martin ◽  
Adewale O. Fadaka ◽  
Nicole R. S. Sibuyi ◽  
Mervin Meyer ◽  
...  

The coronavirus disease 2019 (COVID-19) pandemic has gained worldwide attention and has prompted the development of innovative diagnostics, therapeutics, and vaccines to mitigate the pandemic. Diagnostic methods based on reverse transcriptase-polymerase chain reaction (RT-PCR) technology are the gold standard in the fight against COVID-19. However, this test might not be easily accessible in low-resource settings for the early detection and diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The lack of access to well-equipped clinical laboratories, requirement for the high level of technical competence, and the cost of the RT-PCR test are the major limitations. Moreover, RT-PCR is unsuitable for application at the point-of-care testing (PoCT) as it is time-consuming and lab-based. Due to emerging mutations of the virus and the burden it has placed on the health care systems, there is a growing urgency to develop sensitive, selective, and rapid diagnostic devices for COVID-19. Nanotechnology has emerged as a versatile technology in the production of reliable diagnostic tools for various diseases and offers new opportunities for the development of COVID-19 diagnostic systems. This review summarizes some of the nano-enabled diagnostic systems that were explored for the detection of SARS-CoV-2. It highlights how the unique physicochemical properties of nanoparticles were exploited in the development of novel colorimetric assays and biosensors for COVID-19 at the PoCT. The potential to improve the efficiency of the current assays, as well as the challenges associated with the development of these innovative diagnostic tools, are also discussed.


Biology ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 182 ◽  
Author(s):  
Robin Augustine ◽  
Anwarul Hasan ◽  
Suvarthi Das ◽  
Rashid Ahmed ◽  
Yasuyoshi Mori ◽  
...  

The rampant spread of COVID-19 and the worldwide prevalence of infected cases demand a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. The most common molecular tests approved by regulatory bodies across the world for COVID-19 diagnosis are based on Polymerase Chain Reaction (PCR). While PCR-based tests are highly sensitive, specific, and remarkably reliable, they have many limitations ranging from the requirement of sophisticated laboratories, need of skilled personnel, use of complex protocol, long wait times for results, and an overall high cost per test. These limitations have inspired researchers to search for alternative diagnostic methods that are fast, economical, and executable in low-resource laboratory settings. The discovery of Loop-mediated isothermal Amplification (LAMP) has provided a reliable substitute platform for the accurate detection of low copy number nucleic acids in the diagnosis of several viral diseases, including epidemics like Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). At present, a cocktail of LAMP assay reagents along with reverse transcriptase enzyme (Reverse Transcription LAMP, RT-LAMP) can be a robust solution for the rapid and cost-effective diagnosis for COVID-19, particularly in developing, and low-income countries. In summary, the development of RT-LAMP based diagnostic tools in a paper/strip format or the integration of this method into a microfluidic platform such as a Lab-on-a-chip may revolutionize the concept of PoCT for COVID-19 diagnosis. This review discusses the principle, technology and past research underpinning the success for using this method for diagnosing MERS and SARS, in addition to ongoing research, and the prominent prospect of RT-LAMP in the context of COVID-19 diagnosis.


Author(s):  
Andrea Alemany ◽  
Bàrbara Baro ◽  
Dan Ouchi ◽  
Maria Ubals ◽  
Marc Corbacho-Monné ◽  
...  

AbstractBackgroundThe current standard for COVID-19 diagnosis, RT-qPCR, has important drawbacks for its use as a tool for epidemiological control, including the need of laboratory-processing, high cost, and long turnaround from sampling to results release. Antigen-based rapid diagnostic tests (Ag-RDT) provide a promising alternative for this purpose.MethodsWe assessed the analytical and clinical performance of the Ag-RDT Panbio COVID-19 Ag Test (Abbott), using RT-qPCR as a reference test. The clinical performance was assessed using nasopharyngeal swabs, collected in routine practice for case confirmation and contact tracing, and nasal mid-turbinate swabs, collected in preventive screenings of asymptomatic individuals. Fresh samples were analysed by RT-q-PCR, stored at -80 °C, and analysed using the Ag-RDT according to the manufacturer instructions.FindingsThe Ag-RDT had a limit of detection of 6·5×105 copies/reaction. The clinical performance was assessed on 1,406 frozen swabs with a PCR result available: 951 (67·7%) positive and 455 (32·4%) negative. The Ag-RDT identified the presence of SARS-CoV-2 in 872 of 951 PCR-positive samples (91·7%; 95% CI 89·8-93·4 and ruled out its presence in 450 of 455 PCR-negative samples (specificity 98·9%; 95% CI 97·5– 99·6). Sensitivity increased in samples with lower Ct values (Ct <25, 98·2%; Ct<30, 94·9%) and was higher among symptomatic cases (92·6%) and their contacts (94·2%) than among asymptomatic individuals (79·5%). In the setting of asymptomatic screening, sensitivity also increased with lower Ct values (Ct <25, 100%; Ct<30, 98·6%). Assuming a pre-test probability of 5%, the negative and positive predictive values were 99·6% (99·5 – 99·6) and 81·5% (65·0 – 93·2), respectively.InterpretationThe Panbio COVID-19 Ag-RDT has high sensitivity for detecting the presence of SARS-CoV-2 in nasal or nasopharyngeal swabs of both, symptomatic and asymptomatic individuals. The diagnostic performance of the test is particularly good in samples with viral loads associated with high risk of viral transmission (Ct <25), which show high positive and negative predictive values even when assuming a prevalence as low as 5%.FundingBlueberry diagnostics, Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol, and #YoMeCorono.org crowfunding campaing.Research in contextEvidence before this studyOn October 6, 2020, we searched PubMed for articles containing “Antigen”, “test”, “SARS-CoV-2”, “COVID-19” and “performance” in either the title or the abstract. We found five studies that showed the accuracy of point-of-care tests in identifying SARS-CoV-2 antigens for confirmation of clinically suspected COVID-19. We found high variability in the diagnostic accuracy of Ag-RDT. Most tests showed high specificity (i.e., 99% or higher), whereas sensitivity ranged from 11% to 92%; only one test reported sensitivity higher than 60%. We found no studies investigating the diagnostic accuracy of the Panbio COVID-19 Ag Test. We found no studies that assessed the performance of Ag-RDT for population-level screening of asymptomatic individuals.Added value of this studyOur analysis provides information regarding the diagnostic accuracy of the Panbio COVID-19 Ag Test when tested on 1,406 frozen samples of nasopharyngeal and nasal swabs collected in routine practice for diagnostic confirmation of symptomatic individuals with suspected COVID-19 or contacts exposed to a positive case, and preventive screenings of unexposed asymptomatic individuals. Compared with RT-qPCR as reference test, the Ag-RDT showed a sensitivity and specificity of 91·7% and 98·9%. Test sensitivity increased in samples with viral load associated with high risk of transmission (Ct <25), reaching more than 98%, regardless of the presence of symptoms.Implications of all the available evidenceAvailable evidence show variability in the diagnostic performance of marketed Ag-RDT. Our results provide substantial evidence that the point-of-care Panbio COVID-19 Ag Test can accurately identify SARS-CoV-2 antigens in people with suspected clinical COVID-19 as well as in asymptomatic people with high viral load and therefore, associated with higher risk of transmission. This finding represents a potentially useful advance for mass screening of asymptomatic people at the point-of-care.


2021 ◽  
Vol 19 (1) ◽  
pp. 160-167
Author(s):  
A.E. OJO ◽  
S.O. ADEBAJO ◽  
O.A. OJO ◽  
A.T. AJIBOLA ◽  
D.A. OJO ◽  
...  

Statement of the Problem: Tuberculosis remains a serious public-health threat in developing countries though it has been eradicated in some advanced countries. This disease constitutes a significant threat to global health, being the second highest cause of morbidity and mortality resulting from infectious agents. Prompt diagnosis of active TB facilitates timely therapeutic intervention and minimizes community transmission. Aim: This study aimed at determining a ‘Point of Care’ diagnostic tool for pulmonary tuberculosis (PTB) by comparing the efficiency of four different PTB diagnostic tools for different age groups. Methodology: Zeihl Nelson (ZN) staining, culture, Gene xpert (GX) and Lipoarabinomanan (LAM) assay were employed in this study The culture method was used for confirmation. Sputum and urine samples were collected from each of 100 patients symptomatically diagnosed of PTB. Findings: Fifty-seven percent of the population was male while 43% were female. Mycobacterium tuberculosis was isolated from 9 (9%) of 100 patients. Similarly, GX detected Mycobacterium tuberculosis in 9 (9%) of the patients while the rate of detection using LAM was 10% and with ZN it was 7%. Gene xpert produced no true or false positive and negative result, LAM had one false positive result and ZN had two false negative results. The maximum time frame to generate result was 25 minutes for LAM, two hours for Gene xpert, eight weeks for culture and two days for ZN. Two positive isolates were observed at the same frequency for age group 21-30 and 31- 40 while age groups 1-10, 10-20, 41-50, 50-60 and above has 1 positive result each. Gene xpert had 98.11% sensitivity while LAM had 96.23% and ZN had 86.79%. The choice of ‘Point of Care’ diagnostic tool is of great concern to clinicians and the general public. Conclusion & Significance: This study identified LAM assay as suitable ‘Point of Care’ diagnostic and an add-on tool for PTB diagnosis because of its relatively high sensitivity and short maximum time frame to generate result compare to other three diagnostic techniques.      


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