Multicenter evaluation of the FilmArray Meningitis/Encephalitis assay in a routine setting

2021 ◽  
Vol 70 (10) ◽  
Author(s):  
Karel Maelegheer ◽  
Marijke Reynders ◽  
Katelijne Floré ◽  
Jos Vanacker ◽  
Elke Vanlaere ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Salt Lake ◽  
False Negative ◽  
Salt Lake City ◽  
Hospital Setting ◽  
Ease Of Use ◽  
Added Value ◽  
Clinical Samples ◽  
Routine Diagnostics ◽  
Content Type

Introduction. The FilmArray Meningitis/Encephalitis (FA-ME) Panel (Biofire, Salt Lake City, Utah, US) enables fast and automated detection of 14 pathogens in cerebrospinal fluid (CSF). Gap statement. The performance of the FA-ME panel in a real routine setting has not yet been described and could lead to better patient management in cases of good performance. Aim. This multicenter study verified the FA-ME panel analytical performance in a routine hospital setting. Methodology. Between April 2016 and April 2018, 454 CSF samples were analysed with the FA-ME panel and compared with routine diagnostics. In cases of discrepancy or lack of a comparator result, a profound analysis based on patient records and other laboratory results was performed. Results. A first analysis of 65 frozen samples, suspicious for meningitis had a 89 % concordance with routine diagnostics. The limit of detection (LOD) was confirmed for all pathogens except for Streptococcus agalactiae and a strain of Haemophilus influenzae (Escherichia coli K1 and Cryptococcus gattii LOD experiments were not performed). The routine evaluation showed a positive result in 114 (25 %) clinical samples for at least one target. In three samples co-infections were found. After discrepancy analysis, overall sensitivity was 98 % (false negative FA-ME results for one HSV2, two HSV1 and two parechovirus). Four FA-ME results were considered false positive (two HHV6, one VZV and one E. coli K1), resulting in an overall specificity of >99 %. A clinical added value of the assay was seen in the diagnosis of eight cases of bacterial meningitis. Conclusion. Because of its rapidity and ease of use, the FA-ME panel has great potential in the diagnosis of central nervous infections. Implementation can improve clinical management, but costs and analytical limitations need to be addressed to convince clinicians and laboratories of its value.

scholarly journals Microfluidic Nano-Scale qPCR Enables Ultra-Sensitive and Quantitative Detection of SARS-CoV-2

Processes ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. 1425
Author(s):  
Xin Xie ◽  
Tamara Gjorgjieva ◽  
Zaynoun Attieh ◽  
Mame Massar Dieng ◽  
Marc Arnoux ◽  
...  
Keyword(s):  
Viral Infections ◽  
Limit Of Detection ◽  
False Negative ◽  
False Negative Rate ◽  
Clinical Samples ◽  
Quantitative Detection ◽  
Rt Pcr ◽  
Viral Loads ◽  
Nano Scale ◽  
Negative Rate

A major challenge in controlling the COVID-19 pandemic is the high false-negative rate of the commonly used RT-PCR methods for SARS-CoV-2 detection in clinical samples. Accurate detection is particularly challenging in samples with low viral loads that are below the limit of detection (LoD) of standard one- or two-step RT-PCR methods. In this study, we implemented a three-step approach for SARS-CoV-2 detection and quantification that employs reverse transcription, targeted cDNA preamplification, and nano-scale qPCR based on a commercially available microfluidic chip. Using SARS-CoV-2 synthetic RNA and plasmid controls, we demonstrate that the addition of a preamplification step enhances the LoD of this microfluidic RT-qPCR by 1000-fold, enabling detection below 1 copy/µL. We applied this method to analyze 182 clinical NP swab samples previously diagnosed using a standard RT-qPCR protocol (91 positive, 91 negative) and demonstrate reproducible and quantitative detection of SARS-CoV-2 over five orders of magnitude (<1 to 106 viral copies/µL). Crucially, we detect SARS-CoV-2 with relatively low viral load estimates (<1 to 40 viral copies/µL) in 17 samples with negative clinical diagnosis, indicating a potential false-negative rate of 18.7% by clinical diagnostic procedures. In summary, this three-step nano-scale RT-qPCR method can robustly detect SARS-CoV-2 in samples with relatively low viral loads (<1 viral copy/µL) and has the potential to reduce the false-negative rate of standard RT-PCR-based diagnostic tests for SARS-CoV-2 and other viral infections.

scholarly journals Point-Counterpoint: Meningitis/Encephalitis Syndromic Testing in the Clinical Laboratory

2018 ◽  
Vol 56 (4) ◽  
Author(s):  
Jennifer Dien Bard ◽  
Kevin Alby
Keyword(s):  
Los Angeles ◽  
Clinical Laboratory ◽  
Salt Lake ◽  
Health Care Systems ◽  
False Negative ◽  
Salt Lake City ◽  
Respiratory Pathogens ◽  
Negative Results ◽  
Care Systems ◽  
The University

INTRODUCTION Syndromic panels were first FDA cleared for detection of respiratory pathogens in 2008. Since then, other panels have been approved by the FDA, and most recently, the FilmArray meningitis/encephalitis panel (BioFire, Salt Lake City, UT) has become available. This assay detects 14 targets within 1 h and includes pathogens that typically cause different manifestations of infection, although they infect the same organ system. Several studies have reported both false-positive and false-negative results with this test, and all agree that the cost is significant. As with other panels, health care systems have adopted different strategies for offering this assay. Some have implemented strategies to limit the use of the test to certain patient populations, others have elected not to offer the test, and others have elected not to offer the test and instead request that providers order specific PCRs for the pathogens that best fit the patient's symptoms. In this Point-Counterpoint, Jennifer Dien Bard of the Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, and of the Keck School of Medicine at the University of Southern California explains why laboratories should offer these assays without restriction. Kevin Alby of the University of Pennsylvania explains the concerns about the use of these assays as first-line tests and why some limitations on their use might be appropriate.

scholarly journals False-Negative Rate and Recovery Efficiency Performance of a Validated Sponge Wipe Sampling Method

2011 ◽  
Vol 78 (3) ◽  
pp. 846-854 ◽  
Author(s):  
Paula A. Krauter ◽  
Greg F. Piepel ◽  
Raymond Boucher ◽  
Matt Tezak ◽  
Brett G. Amidan ◽  
...  
Keyword(s):  
Surface Roughness ◽  
Stainless Steel ◽  
Limit Of Detection ◽  
False Negative ◽  
False Negative Rate ◽  
Recovery Efficiency ◽  
Surface Material ◽  
Content Type ◽  
Negative Rate ◽  
Efficiency Performance

ABSTRACTRecovery of spores from environmental surfaces varies due to sampling and analysis methods, spore size and characteristics, surface materials, and environmental conditions. Tests were performed to evaluate a new, validated sponge wipe method usingBacillus atrophaeusspores. Testing evaluated the effects of spore concentration and surface material on recovery efficiency (RE), false-negative rate (FNR), limit of detection (LOD), and their uncertainties. Ceramic tile and stainless steel had the highest mean RE values (48.9 and 48.1%, respectively). Faux leather, vinyl tile, and painted wood had mean RE values of 30.3, 25.6, and 25.5, respectively, while plastic had the lowest mean RE (9.8%). Results show roughly linear dependences of RE and FNR on surface roughness, with smoother surfaces resulting in higher mean REs and lower FNRs. REs were not influenced by the low spore concentrations tested (3.10 × 10−3to 1.86 CFU/cm2). Stainless steel had the lowest mean FNR (0.123), and plastic had the highest mean FNR (0.479). The LOD90(≥1 CFU detected 90% of the time) varied with surface material, from 0.015 CFU/cm2on stainless steel up to 0.039 on plastic. It may be possible to improve sampling results by considering surface roughness in selecting sampling locations and interpreting spore recovery data. Further, FNR values (calculated as a function of concentration and surface material) can be used presampling to calculate the numbers of samples for statistical sampling plans with desired performance and postsampling to calculate the confidence in characterization and clearance decisions.

scholarly journals Are Combined Techniques Using Video Laryngoscopes and Dynamic Stylets Superior to Fiberoptic Techniques for Anticipated Difficult Intubations? A Retrospective Case Control Study

2021 ◽  
Author(s):  
Ashka Shah ◽  
Lauren Knecht ◽  
Cameron Jacobson ◽  
Sean Runnels ◽  
Angela Presson ◽  
...  
Keyword(s):  
Success Rate ◽  
Case Control Study ◽  
Salt Lake ◽  
Salt Lake City ◽  
Ease Of Use ◽  
Retrospective Case ◽  
First Pass ◽  
Lake City ◽  
Combined Technique ◽  
Control Study

Abstract Difficult intubations can require advanced intubation techniques. Studies point to potential advantages of combined techniques using video laryngoscopes (VL) and dynamic stylets for anticipated difficult intubations. This study is designed to compare combined techniques to awake and asleep fiberoptic (FOB) techniques.Methods: 138,387 consecutive anaesthesia cases were reviewed for use of: FOB awake, FOB asleep, or combined technique (VL for visualization and either a FOB or a novel TCITM articulating introducer ((TCITM; Through The Cords, LLC; Salt Lake City, UT)) as dynamic stylets as a primary approach for anticipated difficult intubations. Primary end points measured: first attempt success rate, failure to intubate with the primary technique, “in-room to intubation’ time, reported traumatic intubation rate, and reported ease of intubation.Results: Significant differences were found between techniques. First pass success rate was highest in combined techniques (either VL + FOB or VL + TCITM) (88.7%) followed by FOB awake (74.2%, P<0.001) and FOB asleep (80.7%, P=0.06). “Failure to intubate with the primary technique” was lowest in combined techniques (1.8%) followed by FOB asleep (4.6%, P=0.11) and FOB awake (9.2%, P=0.002). “In room to intubated” time was fastest in combined techniques (13.0 minutes) followed by FOB asleep (15.1 minutes, P=0.002) and FOB awake (21.2 minutes, P<0.001). Combined techniques were rated as ‘easy’ more often (72%) followed by FOB asleep (62.9%, P=0.12) and FOB awake (38.2%, P<0.001). Combined techniques were rated as “atraumatic” more often (91.1%) followed by FOB asleep (89.4%, P=0.91) and FOB awake (75.8%, P<0.001). In subgroup analysis of combined techniques, VL + TCITM had the highest first attempt success rate (90.2%), lowest failure rate (1%, P=0.56), and shortest “in room to intubated time” (12.1 minutes, P=0.12). It was also rated as "easy” (83.3%, P<0.001), and “atraumatic“ (96.1%, P=0.009) more often than VL + FOB, FOB awake or FOB asleep.Conclusions: Combined techniques outperformed FOB techniques in terms of effectiveness, speed, ease of use, and patient injury in patients with risk factors for difficult intubation. As a sub-group of combined technique, VL + TCITM outperformed all other techniques. Combined techniques should be considered when managing difficult intubations.

scholarly journals Low Yield of FilmArray GI Panel in Hospitalized Patients with Diarrhea: an Opportunity for Diagnostic Stewardship Intervention

2017 ◽  
Vol 56 (3) ◽  
Author(s):  
Matthew M. Hitchcock ◽  
Carlos A. Gomez ◽  
Niaz Banaei
Keyword(s):  
Salt Lake ◽  
Diagnostic Yield ◽  
Salt Lake City ◽  
Stool Culture ◽  
False Positives ◽  
Hospitalized Patients ◽  
Adult Patients ◽  
Content Type ◽  
Infectious Gastroenteritis ◽  
Lake City

ABSTRACTThe FilmArray GI panel (BioFire Diagnostics, Salt Lake City, UT) is a multiplex, on-demand, sample-to-answer, real-time PCR assay for the syndromic diagnosis of infectious gastroenteritis that has become widely adopted and, in some instances, has replaced conventional stool culture and parasite exams. Conventional testing has historically been restricted among hospitalized patients due to low diagnostic yield, but it is not known whether use of the FilmArray GI panel should be circumscribed. Cary-Blair stool samples submitted for FilmArray GI panel in adult patients admitted to an academic hospital from August 2015 to January 2017 were included in this study. Of 481 tests performed >72 h after admission, 29 (6.0%) were positive, all for a single target, excludingClostridium difficile. When follow-up tests beyond the first positive per hospitalization were excluded, 20 (4.8%) of 414 tests were positive. There was no difference in yield by immune status. Most targets detected were viral (79% of all positives [n= 23] and 70% in unique patients [n= 14]). All four cases positive for a bacterial target could not be confirmed and presentation was atypical, suggesting possible false positives. After removing potential false positives and chronic viral shedders, the yield was 3.0% (12/406). Repeat testing performed >72 h after admission and following a negative result within the first 72 h was done in 19 patients and 100% (22/22) remained negative. The FilmArray GI panel has low yield in adult patients hospitalized for >72 h, similar to conventional stool microbiology tests, and it is reasonable to restrict its use in this population.

scholarly journals The Malaria TaqMan Array Card Includes 87 Assays for Plasmodium falciparum Drug Resistance, Identification of Species, and Genotyping in a Single Reaction

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Suporn Pholwat ◽  
Jie Liu ◽  
Suzanne Stroup ◽  
Shevin T. Jacob ◽  
Patrick Banura ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Plasmodium Falciparum ◽  
Large Scale ◽  
Limit Of Detection ◽  
Artemisinin Resistance ◽  
Clinical Samples ◽  
Content Type ◽  
Antimalarial Resistance ◽  
Resistance Markers ◽  
Taqman Array

ABSTRACT Antimalarial drug resistance exacerbates the global disease burden and complicates eradication efforts. To facilitate the surveillance of resistance markers in countries of malaria endemicity, we developed a suite of TaqMan assays for known resistance markers and compartmentalized them into a single array card (TaqMan array card, TAC). We included 87 assays for species identification, for the detection of Plasmodium falciparum mutations associated with chloroquine, atovaquone, pyrimethamine, sulfadoxine, and artemisinin resistance, and for neutral single nucleotide polymorphism (SNP) genotyping. Assay performance was first optimized using DNA from common laboratory parasite lines and plasmid controls. The limit of detection was 0.1 to 10 pg of DNA and yielded 100% accuracy compared to sequencing. The tool was then evaluated on 87 clinical blood samples from around the world, and the malaria TAC once again achieved 100% accuracy compared to sequencing and in addition detected the presence of mixed infections in clinical samples. With its streamlined protocol and high accuracy, this malaria TAC should be a useful tool for large-scale antimalarial resistance surveillance.

scholarly journals Effect of Sample Aliquot Size on the Limit of Detection and Reproducibility of Clinical Assays

2007 ◽  
Vol 53 (11) ◽  
pp. 1962-1965 ◽  
Author(s):  
Guorong Chen ◽  
Lori Kobayashi ◽  
Irina Nazarenko
Keyword(s):  
Limit Of Detection ◽  
Probability Model ◽  
False Negative ◽  
Success Probability ◽  
False Negative Rate ◽  
Sample Volume ◽  
Nucleic Acid Amplification ◽  
Clinical Samples ◽  
Minimum Number ◽  
The Impact

Abstract Background: Nucleic acid amplification technologies significantly improved the limit of detection (LOD) for diagnostic assays. The ability of these assays to amplify fewer than 10 target copies of DNA or RNA imposes new requirements on the preparation of clinical samples. We report a statistical method to determine how large of an aliquot is necessary to reproducibly provide a detectable number of cells. Methods: We determined the success probability (p) based on aliquot size and sample volume. The binomial distribution, based on p and the concentration of cells in sample, was used to calculate the probability of getting no target objects in an aliquot and to determine the minimum number of objects per aliquot necessary to generate a reproducible clinical assay. Results: The described method was applied to find a minimum aliquot volume required for a set LOD, false-negative rate (FNR), and %CV. For example, to keep FNR &lt;0.01% for 0.5%, 1% and 2% aliquots (minimum 2000, 1000, and 500 cells per sample) are required. Comparison between experimental and predicted FNR demonstrated good correlation for the small volume aliquots and/or low concentration of target. When 4 μL of 200 copies/mL of plasmid is amplified, predicted and experimental FNRs are 47.2% and 44.9%. Conclusion: This probability model is a useful tool to predict the impact of aliquot volume on the LOD and reproducibility of clinical assays. Even for samples for which pathogens are homogeneously distributed, it is theoretically impossible to collect a single pathogen consistently if the concentration of pathogen is below a certain limit.

RFID in toll/ticketing – a user-centric approach

Info ◽  
2014 ◽  
Vol 16 (6) ◽  
pp. 60-73
Author(s):  
Ardis Storm-Mathisen
Keyword(s):  
Radio Frequency Identification ◽  
Social Practice ◽  
Science And Technology Studies ◽  
Science Studies ◽  
Ease Of Use ◽  
Added Value ◽  
Future Research ◽  
Functional Requirements ◽  
Content Type ◽  
Rfid Applications

Purpose – This article aims to discuss challenges to Radio-Frequency Identification (RFID)-based services from a user perspective located within sociology, anthropology and science and technology studies. Design/methodology/approach – Two cases of toll/ticketing RFID technologies are explored: the mature AutoPASS (tolling on public roads) and the newly implemented Flexus/Ruter Travelcard (public transport) in Norway. A methodologically triangulation of qualitative data is applied to trace the history of RFID implementation, and to compare the benefits proclaimed by suppliers with the hands-on experience of users. Findings – The RFID benefits proclaimed by suppliers were, to a large extent, shared by users in the case of AutoPASS, but to a lesser extent in the case of Flexus/Ruter Travelcard. The cases illustrate that RFID applications are heterogeneous products with different levels of maturity and complexity, applied to fields and services with varied user-groups, functional requirements and privacy concerns. Vital to the success of RFID-based services is good management, compliance with Data Protection Regulations and providing user’s an experience of greater ease-of use and added-value in their everyday lives in comparison to previous systems. Practical implications – Future research should broaden perspectives and methodologies to better grasp the complex interplay among RFID applications, users and the environment. This entails moving beyond a focus on discursive adoption to ethnographic studies of appropriation and how technology affects social practice. Originality/value – RFID is undergoing an extremely expansive usability phase – commercially and socially. Research on RFID is scare and fragmented with few contributions from social science. Studies that privilege user perspectives tend to address the needs and concerns of business rather than of users.

scholarly journals Accuracy of Roche SARS-CoV-2 Rapid Antigen Test in Nasopharyngeal Swab: Clinical Impression Matters

2021 ◽  
Vol 2 (10) ◽  
pp. 929-938
Author(s):  
Khin Phyu Pyar ◽  
Khine Khine Su ◽  
Kyaw Wunna ◽  
Myo Thant ◽  
Kaung Myat ◽  
...  
Keyword(s):  
Predictive Value ◽  
False Negative ◽  
Hospital Setting ◽  
Clinical Samples ◽  
Nasopharyngeal Swab ◽  
Clinical Impression ◽  
Antigen Test ◽  
Rt Pcr ◽  
Ct Value

Background: In COVID-19 pandemic, the diagnosis and treatment must be as early as possible to save the life of each patient. Moreover, screening of asymptomatic carriers, close contacts or healthy subjects must not be delay to prevent transmission to publics. For confirmation of diagnosis of SARS-CoV-2 infection, nasopharyngeal swab must be tested either by real-time Reverse Transcription Polymerase Chain Reaction (RT-PCR) tests or Rapid Antigen Test (RAT). RAT is faster, easier and cheaper; thus, it is suitable for health service in developing country. Objectives: The aim of this study was to assess the diagnostic accuracy of Roche SARS-CoV-2 Rapid Antigen Test (RAT) in diagnosing SARS-CoV-2 infection. Methods: Hospital based exploratory study was done in out-patient department and fever clinic, and molecular laboratory of No. (1) Defence Services General Hospital. Nasopharyngeal swabs were taken, and the Roche SARS- CoV-2 RAT was conducted in parallel with RT-PCR test (reference standard). Results: Among the 932 patients/subjects recruited, RT-PCR was positive in 468 individuals, corresponding to a prevalence of 50.2%. The RAT was positive in 363 patients (60.4%), false positive in 120 patients; it was negative in 569 individuals (39.6%), false negative in 225 patients. The overall sensitivity of the RAT was 51.9% (95% Confidence Interval [CI] 47.29-56.53) and, the specificity was 74.1% (95% CI 69.9-78.07); positive predictive value was 66.9% and negative predictive value was 60.5%. The sensitivity varied with Ct value; 78% in clinical samples with Ct values < 20, 57.5% in those with Ct values between 21 and 25, 41.8% in samples with Ct values between 26 and 30, and, 36.4% in samples with Ct value > 30. Conclusion: The accuracy of the SARS-CoV-2 Roche RAT in diagnosing SARS-CoV-2 infections was inferior to RT-PCR and manufacturer’s data. The sensitivity was with low Cycle threshold values < 20 which were inversely related to the viral load. RAT test should be used in association with clinical impression of physicians. In hospital setting especially in emergency department, the role of RAT should be reconsidered in those patients presenting with anosmia and some cases of dyspnoea, late symptoms in the course of disease, as the RAT results would be false negative. Other errors may arise if the operator for RAT has to handle more than recommended tests per hour especially in the peak of epidemics.

Learning from errors: critical incident reporting in nursing

2017 ◽  
Vol 29 (5) ◽  
pp. 343-356
Author(s):  
Martin Gartmeier ◽  
Eva Ottl ◽  
Johannes Bauer ◽  
Pascal Oliver Berberat
Keyword(s):  
Critical Incident ◽  
Hospital Setting ◽  
Cost Benefit ◽  
Incident Reporting ◽  
Ease Of Use ◽  
Survey Study ◽  
Error Reporting ◽  
Learning From Errors ◽  
Content Type ◽  
Critical Incident Reporting

Purpose The purpose of this paper is to conceptualize error reporting as a strategy for informal workplace learning and investigate nurses’ error reporting cost/benefit evaluations and associated behaviors. Design/methodology/approach A longitudinal survey study was carried out in a hospital setting with two measurements (time 1 [t1]: implementation of a critical incident reporting (CIR) system; t2: three months after t1). Correlational and hierarchical cluster analyses were used to interpret the data. Findings Positive cost-benefit correlations and negative cross-correlations were found, with no substantial changes over time. “Reporters” and “learners” were differentiated regarding error-reporting behaviors. Cost-benefit perceptions predicted membership in the “reporters” group; perception of effort costs negatively predicted an error-reporting preference. Research limitations/implications This study was limited, in that only a questionnaire was used to collect data. Practical implications Stressing the benefits of CIR systems should contribute to reducing employees’ perception of reporting costs; thus, ease of use is a critical factor in CIR system use. Originality/value The study empirically probes a well-established theoretical model, and various ideas for further research are suggested.

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