Project description:Detection of Bordetella pertussis and Bordetella parapertussis using molecular methods is sensitive and specific with a short turnaround time compared to other diagnostic methods. In this multicenter study, we compared the performance of the Simplexa Bordetella Direct kit to those of other molecular assays in detecting and differentiating B. pertussis and B. parapertussis in nasopharyngeal swab specimens. The limits of detection (LODs) were 150 CFU/ml or 3 fg/μl of DNA for B. pertussis and 1,500 CFU/ml or 10 fg/μl of DNA for B. parapertussis A total of 1,103 fresh and residual frozen specimens from eight clinical sites were tested. Combining the data from individual clinical sites using different comparative assays, the overall positive percent agreement (PPA) and negative percent agreement (NPA) for B. pertussis were 98.7% and 97.3%, respectively. The overall PPA and NPA for B. parapertussis were 96.7% and 100%, respectively. For prospective fresh specimens, the overall PPA and NPA for both targets were 97.7% and 99.3%, respectively. For retrospective frozen specimens, the overall PPA and NPA for both targets were 92.6% and 93.2%, respectively. The percentage of invalid results was 1.0%. A cross-reactivity study using 74 non-Bordetella bacterial species and five yeast species revealed that the Simplexa Bordetella Direct kit was 100% specific. The hands-on time and assay run time of the Simplexa Bordetella Direct kit are favorable compared to those of other commercial and laboratory-developed tests. In summary, the Simplexa Bordetella Direct kit has a performance comparable to those of other molecular assays for the detection of B. pertussis and B. parapertussis.
Project description:The Face Mask Wearing Image Dataset is a comprehensive collection of images aimed at facilitating research in the domain of face mask detection and classification. This dataset consists of 24,916 images, carefully categorized into two main folders: "Correct" and "Incorrect" representing instances of face masks being worn properly and improperly, respectively. Each folder is further divided into four subfolders, each denoting a specific type of face mask - Bandana, Cotton, N95, and Surgical. In the "Correct" folder, images depict individuals correctly wearing their respective face masks, while the "Incorrect" folder contains images of improper face mask usage. To capture variations in face mask application across different demographics, such as age and gender, each subfolder also includes three additional subfolders - Child, Male, and Female. The dataset's diverse content encompasses different face mask types, covering bandana-style, cloth, N95 respirators, and surgical masks, across various age groups and genders. This design ensures a comprehensive representation of real-world scenarios, enabling the evaluation of machine learning algorithms for face mask detection and classification. Researchers can leverage this dataset to develop and assess models that can accurately identify and distinguish between correct and incorrect face mask usage. By contributing to the advancement of face mask detection technologies, this dataset further supports public health initiatives and encourages proper mask-wearing behavior to mitigate the spread of infectious diseases, particularly during times of heightened health concerns such as the COVID-19 pandemic.
Project description:Confocal laser endomicroscopy (CLE) allow on-the-fly in vivo intraoperative imaging in a discreet field of view, especially for brain tumors, rather than extracting tissue for examination ex vivo with conventional light microscopy. Fluorescein sodium-driven CLE imaging is more interactive, rapid, and portable than conventional hematoxylin and eosin (H&E)-staining. However, it has several limitations: CLE images may be contaminated with artifacts (motion, red blood cells, noise), and neuropathologists are mainly trained on colorful stained histology slides like H&E while the CLE images are gray. To improve the diagnostic quality of CLE, we used a micrograph of an H&E slide from a glioma tumor biopsy and image style transfer, a neural network method for integrating the content and style of two images. This was done through minimizing the deviation of the target image from both the content (CLE) and style (H&E) images. The style transferred images were assessed and compared to conventional H&E histology by neurosurgeons and a neuropathologist who then validated the quality enhancement in 100 pairs of original and transformed images. Average reviewers' score on test images showed 84 out of 100 transformed images had fewer artifacts and more noticeable critical structures compared to their original CLE form. By providing images that are more interpretable than the original CLE images and more rapidly acquired than H&E slides, the style transfer method allows a real-time, cellular-level tissue examination using CLE technology that closely resembles the conventional appearance of H&E staining and may yield better diagnostic recognition than original CLE grayscale images.
Project description:RT-PCR detection of SARS-CoV-2 mRNA on nasopharyngeal swab is the standard for diagnosing active Covid-19 disease in asymptomatic subjects and in symptomatic patients without the typical radiological findings. Nasopharyngeal swabbing appears a trivial procedure, still an inappropriate nasopharyngeal sampling, performed by untrained operators, can be a relevant cause of false negative findings with a clear negative impact on the effort to control the epidemic and, when PPE is not properly used, this can expose healthcare workers and patients to risks of contagion.
Project description:The use of nasopharyngeal (NP) swab sampling for the detection of various respiratory pathogens has been a standard procedure in medicine for many years. While this is a fairly common procedure, there has been a significant increase in utilization recently due to the SARS-CoV-2 pandemic. We describe a case of a 40-year-old SARS-CoV-2 positive patient with no prior cardiac history who developed asystole while an NP swab was being used to obtain a sample for a SARS-CoV-2 assay. Return of normal sinus rhythm was achieved with chest compressions alone. The incident was deemed to have been an exaggerated vagal response to intranasal stimulation; better known as the trigeminocardiac reflex. This is the first reported case describing asystole during use of an NP swab. This case occurred in a patient with no known cardiac disease and highlights the potential importance of the arrhythmogenic nature of COVID-19 that could potentiate the vagal response in susceptible individuals undergoing NP sampling.
Project description:Objectives/hypothesisNasopharyngeal swabs currently remain the gold standard for COVID-19 sample collection. A surge in testing volume has resulted in a large number of health care workers who are unfamiliar with nasal anatomy performing this test, which can lead to improper collection practices culminating in false-negative results and complications. Therefore, we aimed to assess the accuracy and educational potential of a realistic 3D-printed nasal swab simulator to expedite health care workers' skill acquisition.Study designProspective pre-post interventional study.MethodsA nasal swab task trainer (NSTT) was developed to scale from computed tomography data with a deviated septum. Frontline workers at COVID-19 testing sites in Ontario, Canada, were recruited to use the NSTT for nasopharyngeal swab training. Integrated video recording capability allowed participants to self-evaluate procedure accuracy. A five-point Likert scale was collected regarding the NSTT's educational value and procedural fidelity.ResultsSixty-two frontline workers included in the study were primarily registered nurses (52%) or paramedics (16%). Following simulator use, self-assessed accuracy improved in 77% of all participants and 100% of participants who expressed low confidence before training. Ninety-four percent reported that the NSTT provided a complete educational experience, and 82% regarded the system as a more effective training approach than what is currently available. Eighty-one indicated that the simulator should be used at all COVID-19 testing sites, with 77% stating province-wide implementation was warranted.ConclusionsThe nasal swab task trainer is an effective educational tool that appears well-suited for improved skill acquisition in COVID-19 testing and may be useful for training other nasal swab applications.Level of evidence3 Laryngoscope, 2022.
Project description:Herein, we describe the detection of a SARS-CoV-2 genome through metatranscriptome next-generation sequencing directly from the nasopharyngeal swab of a suspected case of local transmission of Covid-19, in Brazil. Depletion of human ribosomal RNA and use of an optimized in-house developed bioinformatics strategy contributed to successful detection of the virus.
Project description:BackgroundThe current gold standard in coronavirus disease (COVID-19) diagnostics is the real-time reverse transcription-polymerase chain reaction (RT-PCR) assay for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasopharyngeal swab (NPS) samples. Alternatively, nasal swab (NS) or saliva swab (SS) specimens are used, although available data on test accuracy are limited. We examined the diagnostic accuracy of NPS/NS/SS samples for this purpose.MethodsTen patients were included after being tested positive for SARS-CoV-2 RT-PCR in NPS samples according to the National Institute of Infectious Disease guidelines. In comparison with this conventional diagnostic method, NPS/NS/SS samples were tested using the cobas 6800 systems RT-PCR device. To investigate the usefulness of the cobas method and the difference among sample types, the agreement and sensitivity were calculated. Five to six samples were collected over a total period of 5-6 d from each patient.ResultsFifty-seven sets of NPS/NS/SS samples were collected, of which 40 tested positive for COVID-19 by the conventional method. Overall, the concordance rates using the conventional method were 86.0%/70.2%/54.4% for NPS/NS/SS samples (cobas); however, for samples collected up to and including on Day 9 after disease onset (22 negative and one positive specimens), the corresponding rates were 95.7%/87.0%/65.2%. The overall sensitivity estimates were 100.0%/67.5%/37.5% for NPS/NS/SS samples (cobas). For samples up to 9 d after onset, the corresponding values were 100.0%/86.4%/63.6%.ConclusionsNS samples are more reliable than SS samples and can be an alternative to NPS samples. They can be a useful diagnostic method in the future.
Project description:The FilmArray Respiratory Panel 2 (RP2) is a multiplex in vitro diagnostic test for the simultaneous and rapid (?45-min) detection of 22 pathogens directly from nasopharyngeal swab (NPS) samples. It contains updated (and in some instances redesigned) assays that improve upon the FilmArray Respiratory Panel (RP; version 1.7), with a faster run time. The organisms identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus, human rhinovirus/enterovirus, influenza virus A, influenza virus A H1, influenza virus A H1-2009, influenza virus A H3, influenza virus B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, respiratory syncytial virus, Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae Two new targets are included in the FilmArray RP2: Middle East respiratory syndrome coronavirus and Bordetella parapertussis This study provides data from a multicenter evaluation of 1,612 prospectively collected NPS samples, with performance compared to that of the FilmArray RP or PCR and sequencing. The overall percent agreement between the FilmArray RP2 and the comparator testing was 99.2%. The RP2 demonstrated a positive percent agreement of 91.7% or greater for detection of all but three analytes: coronavirus OC43, B. parapertussis, and B. pertussis The FilmArray RP2 also demonstrated a negative percent agreement of ?93.8% for all analytes. Of note, the adenovirus assay detects all genotypes, with a demonstrated increase in sensitivity. The FilmArray RP2 represents a significant improvement over the FilmArray RP, with a substantially shorter run time that could aid in the diagnosis of respiratory infections in a variety of clinical scenarios.