Saliva has garnered great interest as an alternative specimen type for molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Data are limited on the relative ...performance of different molecular methods using saliva specimens and the relative sensitivity of saliva to nasopharyngeal (NP) swabs.
To address the gap in knowledge, we enrolled symptomatic healthcare personnel (n = 250) from Barnes-Jewish Hospital/Washington University Medical Center and patients presenting to the Emergency Department with clinical symptoms compatible with coronavirus disease 2019 (COVID-19; n = 292). We collected paired saliva specimens and NP swabs. The Lyra SARS-CoV-2 assay (Quidel) was evaluated on paired saliva and NP samples. Subsequently we compared the Simplexa COVID-19 Direct Kit (Diasorin) and a modified SalivaDirect (Yale) assay on a subset of positive and negative saliva specimens.
The positive percent agreement (PPA) between saliva and NP samples using the Lyra SARS-CoV-2 assay was 63.2%. Saliva samples had higher SARS-CoV-2 cycle threshold values compared to NP swabs (P < 0.0001). We found a 76.47% (26/34) PPA for Simplexa COVID-19 Direct Kit on saliva and a 67.6% (23/34) PPA for SalivaDirect compared to NP swab results.
These data demonstrate molecular assays have variability in performance for detection of SARS-CoV-2 in saliva.
With more than 900,000 confirmed cases worldwide and nearly 50,000 deaths during the first 3 months of 2020, the coronavirus disease 2019 (COVID-19) pandemic has emerged as an unprecedented health ...care crisis. The spread of COVID-19 has been heterogeneous, resulting in some regions having sporadic transmission and relatively few hospitalized patients with COVID-19 and others having community transmission that has led to overwhelming numbers of severe cases. For these regions, health care delivery has been disrupted and compromised by critical resource constraints in diagnostic testing, hospital beds, ventilators, and health care workers who have fallen ill to the virus exacerbated by shortages of personal protective equipment. Although mild cases mimic common upper respiratory viral infections, respiratory dysfunction becomes the principal source of morbidity and mortality as the disease advances. Thoracic imaging with chest radiography and CT are key tools for pulmonary disease diagnosis and management, but their role in the management of COVID-19 has not been considered within the multivariable context of the severity of respiratory disease, pretest probability, risk factors for disease progression, and critical resource constraints. To address this deficit, a multidisciplinary panel comprised principally of radiologists and pulmonologists from 10 countries with experience managing patients with COVID-19 across a spectrum of health care environments evaluated the utility of imaging within three scenarios representing varying risk factors, community conditions, and resource constraints. Fourteen key questions, corresponding to 11 decision points within the three scenarios and three additional clinical situations, were rated by the panel based on the anticipated value of the information that thoracic imaging would be expected to provide. The results were aggregated, resulting in five main and three additional recommendations intended to guide medical practitioners in the use of chest radiography and CT in the management of COVID-19.
Upper respiratory tract infections are common, and the ability to accurately and rapidly diagnose the causative pathogen has important implications for patient management.
We evaluated the ...test-ordering practices for 2 commonly utilized nucleic acid amplification tests (NAATs) for the detection of respiratory pathogens: the Xpert Flu Assay for influenza A/B (Flu assay) and the Biofire FilmArray respiratory panel assay (RP assay), which detects 20 different targets. Our study examined repeat testing; that is, testing within 7 days from an initial test.
Our study found that repeat testing is common for each of the individual assays: 3.0% of all Flu assays and 10.0% of all RP assays were repeat testing. Of repeat testing, 8/293 (2.7%) of repeat Flu assays and 75/1257 (6.0%) of RP assays resulted diagnostic gains, i.e., new detections. However, for the RP assay, these new detections were not always clinically actionable. The most frequently discrepant organisms were rhinovirus/enterovirus (28/102, 27.5%), followed by respiratory syncytial virus (12/102, 11.8%) and coronavirus OC43 (11/102, 10.8%). Furthermore, there were 3,336 instances in which a patient was tested using both a Flu assay and RP assay, of which only 44 (1.3%) had discrepant influenza results.
Our findings suggest opportunities exist to better guide ordering practices for respiratory pathogen testing, including limiting repeat testing, with the goal of optimization of clinical yield, and diagnostic stewardship.
Abstract
Background
The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patient samples is of critical importance in the management of patients and monitoring ...transmission in the population. However, data on the analytical performance characteristics for detection of SARS-CoV-2 in clinical specimens between individual targets within the same platform, and among different analytical platforms, are limited.
Methods
Here we evaluated the performance of 6 different sample-to-answer SARS-CoV-2 detection methods—Roche cobas 6800, Cepheid GeneXpert, Diasorin Simplexa, Luminex Aries emergency use authorization (EUA), Luminex Aries research use only (RUO), and bioMérieux BioFire—in clinical specimens with a range of viral loads.
Results
The positive percentage agreement between the Roche cobas 6800 and GeneXpert was 100%, Diasorin 95%, Aries EUA 74%, Aries RUO 83%, and BioFire 97%. Notably, in samples with cycle threshold (Ct) values below 30 for the E gene on the Roche cobas 6800 platform, we found 100% positive agreement among all platforms. Given these results, we examined the distribution of over 10 000 Ct values of all positive specimens from individuals at our institution on the Roche cobas platform. Nearly 60% of specimens from asymptomatic individuals had a PCR Ct value >30 as measured using the cobas 6800 assay E gene.
Conclusions
Our results demonstrate performance characteristics between different platforms by Ct value and provide data regarding the distribution of viral RNA present in positive specimens.
Abstract Current diagnostic methods for dengue virus (DV) rely primarily on detection of anti-DV antibodies and/or DV RNA by reverse transcriptase (RT) PCR. Several limitations exist however: ...seroconversion is delayed following infection, and DV RT-PCR assays are not yet readily available. The DV nonstructural protein 1 (NS1) antigen is an alternative acute phase DV biomarker, and here, we evaluated the new InBios (InBios International, Inc., Seattle, WA, USA) DENV DetectTM NS1 enzyme-linked immunoassay (ELISA) compared to DV RT-PCR and serology for detection of recent DV infection. We report a positive, negative, and overall percent agreement of 96% (24/25), 86.0% (43/50), and 89.3% (67/75) for the InBios NS1 ELISA compared to DV RT-PCR. Performance of the NS1 ELISA compared to serology for anti-DV IgM antibodies showed a positive, negative, and overall percent agreement of 78.0% (85/109), 90.7% (333/367), and 87.8% (418/476), respectively. Collectively, the InBios NS1 ELISA can be used as an alternative to DV RT-PCR for identification of acute DV infection.
Microsporidiosis is an emerging opportunistic infection in immunocompromised patients. We report a case of fatal disseminated Anncaliia algerae infection in a profoundly immunosuppressed pancreas and ...kidney transplant recipient.
Abstract Background In contrast with recurrent unipolar depression, relatively little is known about the seasonality of depressive episodes in bipolar affective disorder (BAD). Method We compared ...responses on the Seasonal Pattern Assessment Questionnaire (SPAQ) between a cohort of 183 patients with BAD and a large sample of patients in primary care (N = 4746). Comparisons were adjusted for age and gender. Results 27% of the BAD patients fulfilled SPAQ criteria for Seasonal Affective Disorder (SAD. This gave an adjusted odds ratio of 3.73 (95% confidence intervals 2.64 to 5.27) in comparison with the rate among the primary care samples. Global seasonality scores were significantly higher among BAD patients (adjusted mean difference 1.73, 95% CI 0.97 to 2.49, p < 0.001). Limitations The SPAQ was originally designed as a screening instrument rather than as a case-finding instrument. Conclusions Vigilance for seasonal symptom recurrence in BAD may be important with regard to management and relapse prevention.
Abstract Two automated systems, BD Phoenix and bioMérieux Vitek 2, were compared to a double-disk diffusion method for the detection of inducible resistance to clindamycin in Staphylococcus spp. ...Analysis of 524 clinical isolates revealed sensitivity and specificity of 100% and 99.6%, respectively, for Phoenix and 91.1% and 99.8%, respectively, for Vitek 2.
ABSTRACT
An article in this issue of the
Journal of Clinical Microbiology
(J.-H. Youn, S. K. Drake, R. A. Weingarten, K. M. Frank, J. P. Dekker, and A. F. Lau, J Clin Microbiol 53:35–42, 2015,
...http://dx.doi.org/10.1128/JCM.01643-15
) describes the use of matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry for the detection of organisms carrying a
bla
KPC
-containing plasmid. This powerful and promising application highlights the challenges of using MALDI-TOF mass spectrometry for purposes other than organism identification.
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