scholarly journals An automated Dashboard to improve laboratory COVID-19 diagnostics management

2021 ◽  
Author(s):  
Emma Maury ◽  
Marc-Olivier Boldi ◽  
Gilbert Greub ◽  
Valerie Chavez ◽  
Katia Jaton ◽  
...  
Keyword(s):  
Influenza A ◽  
Data Extraction ◽  
Resource Planning ◽  
Added Value ◽  
University Hospital ◽  
Molecular Diagnostic ◽  
Rt Pcr ◽  
Diagnostic Laboratory ◽  
R Shiny ◽  
And Gender

Background: In response to the CoVID-19 pandemic, our microbial diagnostic laboratory located in a university hospital has implemented several distinct SARS-CoV-2 RT-PCR systems in a very short time. Thanks to our automated molecular diagnostic platform, more than 140 000 SARS-CoV-2 RT-PCR tests were achieved over 12 months, with peaks higher than 1 500 daily tests. A dashboard was developed to give access to Key Performance Indicators (KPIs) to improve laboratory operational management. Methods: RT-PCR data extraction of four respiratory viruses - SARS-CoV-2, influenza A and B and RSV - from our laboratory information system (LIS), was automated. Important KPIs were identified and the visualization was achieved using an in-house dashboard based on the open-source language R (Shiny). Information is updated every 4 hours. Results: The dashboard is organized into three main parts. The Filter page presents all the KPIs, divided into five sections: i) general and gender-related indicators, ii) number of tests and positivity rate, iii) cycle threshold and viral load, iv) test durations, and v) not valid results. Filtering allows to select a given period, a dedicated instrument, a given specimen, or a requester for instance. The Comparison page allows a custom charting of all the available variables, which represents more than 182 combinations. The Data page gives the user access to the raw data in table format, with the possibility of filtering, allowing for a deeper analysis and data download in Excel format. Conclusions: The dashboard, that gives a rapid access to a huge number of up-to-date information, represents a reliable and user-friendly tool improving the decision-making process, resource planning and quality management. The dashboard represent an added value for diagnosric laboratories during a pandemic, where rapid and efficient adaptation is mandatory.

scholarly journals An Automated Dashboard to Improve Laboratory COVID-19 Diagnostics Management

2021 ◽  
Vol 3 ◽  
Author(s):  
Emma Maury ◽  
Marc-Olivier Boldi ◽  
Gilbert Greub ◽  
Valérie Chavez ◽  
Katia Jaton ◽  
...  
Keyword(s):  
Influenza A ◽  
Data Extraction ◽  
Resource Planning ◽  
Test Reliability ◽  
University Hospital ◽  
Sample Type ◽  
Rt Pcr ◽  
Diagnostic Laboratory ◽  
And Gender ◽  
User Friendly

Background: In response to the COVID-19 pandemic, our microbial diagnostic laboratory located in a university hospital has implemented several distinct SARS-CoV-2 RT-PCR systems in a very short time. More than 148,000 tests have been performed over 12 months, which represents about 405 tests per day, with peaks to more than 1,500 tests per days during the second wave. This was only possible thanks to automation and digitalization, to allow high throughput, acceptable time to results and to maintain test reliability. An automated dashboard was developed to give access to Key Performance Indicators (KPIs) to improve laboratory operational management.Methods: RT-PCR data extraction of four respiratory viruses—SARS-CoV-2, influenza A and B and RSV—from our laboratory information system (LIS), was automated. This included age, gender, test result, RT-PCR instrument, sample type, reception time, requester, and hospitalization status etc. Important KPIs were identified and the visualization was achieved using an in-house dashboard based on the open-source language R (Shiny).Results: The dashboard is organized into three main parts. The “Filter” page presents all the KPIs, divided into five sections: (i) general and gender-related indicators, (ii) number of tests and positivity rate, (iii) cycle threshold and viral load, (iv) test durations, and (v) not valid results. Filtering allows to select a given period, a dedicated instrument, a given specimen, an age range or a requester. The “Comparison” page allows a custom charting of all the available variables, which represents more than 182 combination. The “Data” page, gives the user an access to the raw data in tables format, with possibility of filtering, allowing for a deeper analysis and data download. Informations are updated every 4 h.Conclusions: By giving a rapid access to a huge number of up-to-date information, represented using the most relevant visualization types, without the burden of timely data extraction and analysis, the dashboard represents a reliable and user-friendly tool for operational laboratory management. The dashboard represents a reliable and user-friendly tool improving the decision-making process, resource planning and quality management.

1376: Molecular Diagnostic Detection of Haploid Germ Cells in Testicular Biopsy Specimens by Online RT-PCR

2004 ◽  
Vol 171 (4S) ◽  
pp. 362-363
Author(s):  
Mark G. Schrader ◽  
Markus Muller ◽  
Wolfgang Schulze ◽  
Steffen Weikert ◽  
Kurt Miller
Keyword(s):  
Germ Cells ◽  
Testicular Biopsy ◽  
Molecular Diagnostic ◽  
Rt Pcr ◽  
Biopsy Specimens ◽  
Diagnostic Detection

scholarly journals Molecular Detection of Mycobacterium tuberculosis in Oral Mucosa from Patients with Presumptive Tuberculosis

2020 ◽  
Vol 9 (12) ◽  
pp. 4124
Author(s):  
Barbara Molina-Moya ◽  
Nelly Ciobanu ◽  
Marta Hernandez ◽  
Cristina Prat-Aymerich ◽  
Valeriu Crudu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Oral Mucosa ◽  
The Elderly ◽  
Storage Conditions ◽  
Molecular Diagnostic ◽  
Smear Microscopy ◽  
X Rays ◽  
Rt Pcr ◽  
Tuberculosis Complex ◽  
Tb 34

Tuberculosis (TB) diagnosis is increasingly based on the detection of Mycobacterium tuberculosis complex (MTBC) DNA in sputum using molecular diagnostic tests as the first test for diagnosis. However, sputum can be difficult to obtain in children, patients without productive cough, and the elderly and approaches testing non-sputum samples are needed. We evaluated whether TB can be detected from the oral mucosa of patients with TB. Adults with presumptive TB were examined using culture, Xpert MTB/RIF, smear microscopy and X-Rays. Oral mucosa swabs collected on PrimeStore-MTM, stored at room temperature if tested within 30 days or at −20 °C if examined at a later time. RT-PCR was performed to detect M. tuberculosis DNA. Eighty patients had bacteriologically-confirmed TB, 34 had bacteriologically-negative TB (negative tests but abnormal X-rays) and 152 were considered not to have TB (not TB). Oral swabs RT-PCR were positive in 29/80 (36.3%) bacteriologically-confirmed, 9/34 (26.5%) bacteriologically-negative and 29/152 (19.1%) not TB. The yield varied among samples stored for less and more than 30 days (p = 0.013) from 61% (11/18) and 29% (18/62) among bacteriologically confirmed, and 30.8% (4/13) and 23.8% (5/21) among bacteriologically-negative participants. Among not TB patients, the specificity was 80.9% (123/152), being 78.3% (18/23) among samples stored less than 30 days and 81.4% (105/129) among samples stored for more than 30 days (p = 0.46). The detection of M. tuberculosis in oral mucosa samples is feasible, but storage conditions may affect the yield.

scholarly journals Implementing SARS-CoV-2 Rapid Antigen Testing in the Emergency Ward of a Swiss University Hospital: The INCREASE Study

2021 ◽  
Vol 9 (4) ◽  
pp. 798
Author(s):  
Giorgia Caruana ◽  
Antony Croxatto ◽  
Eleftheria Kampouri ◽  
Antonios Kritikos ◽  
Onya Opota ◽  
...  
Keyword(s):  
Immunoglobulin A ◽  
University Hospital ◽  
Lower Sensitivity ◽  
Clinical Settings ◽  
Rt Pcr ◽  
Emergency Ward ◽  
Viral Loads ◽  
Asymptomatic Patients ◽  
Asymptomatic Subjects ◽  
Antigen Testing

Following the Swiss Federal Office of Public Health (FOPH) authorization of the rapid antigen test (RAT), we implemented the use of the RAT in the emergency ward of our university hospital for patients’ cohorting. RAT triaging in association with RT-PCR allowed us to promptly isolate positive patients and save resources. Among 532 patients, overall sensitivities were 48.3% for Exdia and 41.2% for Standard Q®, PanbioTM and BD Veritor™. All RATs exhibited specificity above 99%. Sensitivity increased to 74.6%, 66.2%, 66.2% and 64.8% for Exdia, Standard Q®, PanbioTM and BD Veritor™, respectively, for viral loads above 105 copies/mL, to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/mL and 100% for viral loads above 107 copies/mL. Sensitivity was significantly higher for patients with symptoms onset within four days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with the evolution of symptoms longer than four days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Among COVID-19 asymptomatic patients, sensitivity was 33%. All Immunoglobulin-A-positive patients resulted negative for RAT. The RAT might represent a useful resource in selected clinical settings as a complementary tool in RT-PCR for rapid patient triaging, but the lower sensitivity, especially in late presenters and COVID-19 asymptomatic subjects, must be taken into account.

scholarly journals Effects of the COVID-19 Epidemic on Hospital Admissions for Non-Communicable Diseases in a Large Italian University-Hospital: A Descriptive Case-Series Study

2021 ◽  
Vol 10 (4) ◽  
pp. 880
Author(s):  
Caterina Caminiti ◽  
Giuseppe Maglietta ◽  
Tiziana Meschi ◽  
Andrea Ticinesi ◽  
Mario Silva ◽  
...  
Keyword(s):  
Hospital Admissions ◽  
Case Series ◽  
Communicable Diseases ◽  
University Hospital ◽  
Negative Consequences ◽  
Non Communicable Diseases ◽  
Case Series Study ◽  
And Gender ◽  
Long Term Impact ◽  
Series Study

Background: Concern is growing about the negative consequences that response measures to the COVID-19 epidemic may have on the management of other medical conditions. Methods: A retrospective descriptive case-series study conducted at a large University-hospital in northern Italy, an area severely hit by the epidemic. Results: Between 23 February and 14 May 2020, 4160 (52%) COVID-19 and 3778 (48%) non-COVID-19 patients were hospitalized. COVID-19 admissions peaked in the second half of March, a period characterized by an extremely high mortality rate (27.4%). The number of admissions in 2020 was similar to 2019, but COVID-19 patients gradually occupied all available beds. Comparison between COVID-19 and non-COVID-19 admissions in 2020 revealed significant differences concerning all age classes and gender. Specifically, COVID-19 patients were older, predominantly male, and exhibited more comorbidities. Overall, admissions for non-communicable diseases (NCDs) in 2020 vs. 2019 dropped by approximately one third. Statistically significant reductions were observed for acute myocardial infarction (−78, −33.9%), cerebrovascular disease (−235, −41.5%), and cancer (−368, −31.9%). While the first two appeared equally distributed between COVID-19 and non-COVID-19 patients, chronic NCDs were statistically significantly more frequent in the former, except cancer, which was less frequent in COVID-19 patients. Conclusions: Prevention of collateral damage to patients with other diseases should be an integral part of epidemic response plans. Prospective cohort studies are needed to understand the long-term impact.

scholarly journals Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ramesh Yelagandula ◽  
◽  
Aleksandr Bykov ◽  
Alexander Vogt ◽  
Robert Heinen ◽  
...  
Keyword(s):  
Influenza A ◽  
Respiratory Infections ◽  
High Sensitivity ◽  
Cost Effective ◽  
Massively Parallel ◽  
Rt Pcr ◽  
Viral Spread ◽  
Saliva Analysis ◽  
Double Blinded ◽  
Generation Sequencing

AbstractThe COVID-19 pandemic has demonstrated the need for massively-parallel, cost-effective tests monitoring viral spread. Here we present SARSeq, saliva analysis by RNA sequencing, a method to detect SARS-CoV-2 and other respiratory viruses on tens of thousands of samples in parallel. SARSeq relies on next generation sequencing of multiple amplicons generated in a multiplexed RT-PCR reaction. Two-dimensional, unique dual indexing, using four indices per sample, enables unambiguous and scalable assignment of reads to individual samples. We calibrate SARSeq on SARS-CoV-2 synthetic RNA, virions, and hundreds of human samples of various types. Robustness and sensitivity were virtually identical to quantitative RT-PCR. Double-blinded benchmarking to gold standard quantitative-RT-PCR performed by human diagnostics laboratories confirms this high sensitivity. SARSeq can be used to detect Influenza A and B viruses and human rhinovirus in parallel, and can be expanded for detection of other pathogens. Thus, SARSeq is ideally suited for differential diagnostic of infections during a pandemic.

scholarly journals Development and application of a real-time RT-PCR assay to rapidly detect H2 subtype avian influenza A viruses

2021 ◽  
pp. 104063872199481
Author(s):  
Yixin Xiao ◽  
Fan Yang ◽  
Fumin Liu ◽  
Hangping Yao ◽  
Nanping Wu ◽  
...  
Keyword(s):  
Avian Influenza ◽  
Real Time ◽  
Influenza A ◽  
Minor Groove Binder ◽  
Rt Pcr ◽  
Influenza A Viruses ◽  
Pcr Assay ◽  
Infectious Dose ◽  
The Matrix ◽  
Taqman Minor Groove Binder

The H2 subtypes of avian influenza A viruses (avian IAVs) have been circulating in poultry, and they have the potential to infect humans. Therefore, establishing a method to quickly detect this subtype is pivotal. We developed a TaqMan minor groove binder real-time RT-PCR assay that involved probes and primers based on conserved sequences of the matrix and hemagglutinin genes. The detection limit of this assay was as low as one 50% egg infectious dose (EID50)/mL per reaction. This assay is specific, sensitive, and rapid for detecting avian IAV H2 subtypes.

scholarly journals The role of CT imaging for management of COVID-19 in epidemic area: early experience from a University Hospital

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Vikram rao Bollineni ◽  
Koenraad Hans Nieboer ◽  
Seema Döring ◽  
Nico Buls ◽  
Johan de Mey
Keyword(s):  
Ct Scan ◽  
Predictive Value ◽  
Ct Imaging ◽  
Chest Ct ◽  
University Hospital ◽  
Rt Pcr ◽  
Ct Findings ◽  
Epidemic Area ◽  
Chest Ct Scan ◽  
Pcr Test

Abstract Background To evaluate the clinical value of the chest CT scan compared to the reference standard real-time polymerase chain reaction (RT-PCR) in COVID-19 patients. Methods From March 29th to April 15th of 2020, a total of 240 patients with respiratory distress underwent both a low-dose chest CT scan and RT-PCR tests. The performance of chest CT in diagnosing COVID-19 was assessed with reference to the RT-PCR result. Two board-certified radiologists (mean 24 years of experience chest CT), blinded for the RT-PCR result, reviewed all scans and decided positive or negative chest CT findings by consensus. Results Out of 240 patients, 60% (144/240) had positive RT-PCR results and 89% (213/240) had a positive chest CT scans. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of chest CT in suggesting COVID-19 were 100% (95% CI: 97–100%, 144/240), 28% (95% CI: 19–38%, 27/240), 68% (95% CI: 65–70%) and 100%, respectively. The diagnostic accuracy of the chest CT suggesting COVID-19 was 71% (95% CI: 65–77%). Thirty-three patients with positive chest CT scan and negative RT-PCR test at baseline underwent repeat RT-PCR assay. In this subgroup, 21.2% (7/33) cases became RT-PCR positive. Conclusion Chest CT imaging has high sensitivity and high NPV for diagnosing COVID-19 and can be considered as an alternative primary screening tool for COVID-19 in epidemic areas. In addition, a negative RT-PCR test, but positive CT findings can still be suggestive of COVID-19 infection.

scholarly journals A Machine Learning Model Incorporating Laboratory Blood Tests Discriminates Between SARS-CoV-2 and Influenza Infections at Emergency Department Visit

2021 ◽  
Author(s):  
Junyi Liu ◽  
Lars F Westblade ◽  
Amy Chadburn ◽  
Richard Fideli ◽  
Arryn Craney ◽  
...  
Keyword(s):  
Emergency Department ◽  
Laboratory Test ◽  
Calcium Level ◽  
Influenza A ◽  
Respiratory Pathogens ◽  
Rt Pcr ◽  
Blood Tests ◽  
Laboratory Test Results ◽  
Presentation Methods ◽  
The Impact

Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus are contagious respiratory pathogens with similar symptoms but require different treatment and management strategies. This study investigated whether laboratory blood tests can discriminate between SARS-CoV-2 and influenza infections at emergency department (ED) presentation. Methods: 723 influenza A/B positive (2018/1/1 to 2020/3/15) and 1,281 SARS-CoV-2 positive (2020/3/11 to 2020/6/30) ED patients were retrospectively analyzed. Laboratory test results completed within 48 hours prior to reporting of virus RT-PCR results, as well as patient demographics were included to train and validate a random forest (RF) model. The dataset was randomly divided into training (2/3) and testing (1/3) sets with the same SARS-CoV-2/influenza ratio. The Shapley Additive Explanations technique was employed to visualize the impact of each laboratory test on the differentiation. Results: The RF model incorporating results from 15 laboratory tests and demographic characteristics discriminated SARS-CoV-2 and influenza infections, with an area under the ROC curve value 0.90 in the independent testing set. The overall agreement with the RT-PCR results was 83% (95% CI: 80-86%). The test with the greatest impact on the differentiation was serum total calcium level. Further, the model achieved an AUC of 0.82 in a new dataset including 519 SARS-CoV-2 ED patients (2020/12/1 to 2021/2/28) and the previous 723 influenza positive patients. Serum calcium level remained the most impactful feature on the differentiation. Conclusion: We identified characteristic laboratory test profiles differentiating SARS-CoV-2 and influenza infections, which may be useful for the preparedness of overlapping COVID-19 resurgence and future seasonal influenza.

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