The urgent need to implement and rapidly expand testing for severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection has led to the development of multiple assays. How these tests ...perform relative to one another is poorly understood. We evaluated the concordance between the Roche Diagnostics cobas 6800 SARS‐CoV‐2 test and a laboratory‐developed test (LDT) real‐time reverse transcription‐polymerase chain reaction based on a modified Centers for Disease Control and Prevention protocol, for the detection of SARS‐CoV‐2 in samples submitted to the Clinical Laboratories of the Mount Sinai Health System. A total of 1006 nasopharyngeal swabs in universal transport medium from persons under investigation were tested for SARS‐CoV‐2 as part of routine clinical care using the cobas SARS‐CoV‐2 test with subsequent evaluation by the LDT. Cycle threshold values were analyzed and interpreted as either positive (“detected” or “presumptive positive”), negative (not detected), inconclusive, or invalid. Statistical analysis was performed using GraphPad Prism 8. The cobas SARS‐CoV‐2 test reported 706 positive and 300 negative results. The LDT reported 640 positive, 323 negative, 34 inconclusive, and 9 invalid results. When excluding inconclusive and invalid results, the overall percent agreement between the two platforms was 95.8%. Cohen's κ coefficient was 0.904 (95% confidence interval, 0.875‐0.933), suggesting almost perfect agreement between both platforms. An overall discordance rate of 4.2% between the two systems may reflect differences in primer sequences, assay limit of detection, or other factors, highlighting the importance of comparing the performance of different testing platforms.
Highlights
In this study, we compared the detection of SARS‐CoV‐2 in clinical samples from patients being evaluated for CoVID‐19 infection by two different RT‐PCR assays, the cobas® 6800 SARS‐CoV‐2 test from Roche Molecular Systems and a laboratory‐developed test (LDT) using the Centers for Disease Control and Prevention 2019‐nCoV primers and probes. Overall there was excellent agreement between the two tests methods, although our results suggest that the cobas® SARSCoV‐2 test may have a lower limit of detection than the LDT.
Abstract
Numerous reports document the spread of SARS-CoV-2, but there is limited information on its introduction before the identification of a local case. This may lead to incorrect assumptions ...when modeling viral origins and transmission. Here, we utilize a sample pooling strategy to screen for previously undetected SARS-CoV-2 in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across the Mount Sinai Health System in New York. The patients had been previously evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We identify SARS-CoV-2 RNA from specimens collected as early as 25 January 2020, and complete SARS-CoV-2 genome sequences from multiple pools of samples collected between late February and early March, documenting an increase prior to the later surge. Our results provide evidence of sporadic SARS-CoV-2 infections a full month before both the first officially documented case and emergence of New York as a COVID-19 epicenter in March 2020.
Febrile neutropenia (FN) is a medical emergency with significant morbidity and mortality for oncology patients, requiring comprehensive workup and timely antibiotic administration. We evaluated ...concordance with locally developed FN guidelines and outcomes of cancer patients admitted to general internal medicine at an academic teaching hospital.
We conducted a retrospective observational cohort study of patients admitted between July 1, 2016, and June 30, 2017, for FN. Patients were classified as having low-risk or high-risk FN according to their malignancy and chemotherapy. Primary outcome was the proportion of patients receiving guideline-concordant antibiotics within 48 hours of admission to general internal medicine. Secondary outcomes were the proportion of patients in whom empirical antibiotics were active against pathogens isolated, rate of antibiotic-associated adverse events, and in-hospital mortality. We used logistic regression to model relationship between FN risk and guideline-concordant antibiotics.
Among 100 patients included, 34 (34%) were low-risk FN and 66 (66%) were high-risk. Proportion of guideline-concordant empirical antibiotics was significantly lower among low-risk FN patients than high-risk patients: 12 (35%) of 34 versus 47 (71%) of 66 (
= .001). Empirical antibiotics were active against 17 (94%) of 18 isolated pathogens. The mortality rate was 3%, and 16% of patients experienced antibiotic-associated adverse events. Hematological malignancy and infectious diseases-trained physician involvement were associated with guideline-concordant prescribing, with adjusted odds ratios of 3.76 (95% CI, 1.46-9.70;
= .006) and 3.71 (95% CI, 1.49-9.23;
= .005), respectively.
Guideline concordance was low compared to published reports. Factors influencing appropriate antimicrobial prescribing in patients with FN warrant further exploration.
The emergence and rapid proliferation of Coronavirus Disease-2019, throughout the past year, has put an unprecedented strain on the global schema of health infrastructure and health economy. The ...time-sensitive agenda of identifying the virus in humans and delivering a vaccine to the public constituted an effort to flatten the statistical curve of viral spread as it grew exponentially. At the forefront of this effort was an exigency of developing rapid and accurate diagnostic strategies. These have emerged in various forms over the past year-each with strengths and weaknesses. To date, they fall into three categories: (1) those isolating and replicating viral RNA in patient samples from the respiratory tract (Nucleic Acid Amplification Tests; NAATs), (2) those detecting the presence of viral proteins (Rapid Antigen Tests; RATs) and serology-based exams identifying antibodies to the virus in whole blood and serum. The latter vary in their detection of immunoglobulins of known prevalence in early-stage and late-stage infection. With this review, we delineate the categories of testing measures developed to date, analyze the efficacy of collecting patient specimens from diverse regions of the respiratory tract, and present the up and coming technologies which have made pathogen identification easier and more accessible to the public.
There is concern that the global burden of coronavirus disease of 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection might yield an increased occurrence of ...Guillain-Barré syndrome (GBS). It is currently unknown whether concomitant SARS-CoV-2 infection and GBS are pathophysiologically related, what biomarkers are useful for diagnosis, and what is the optimal treatment given the medical comorbidities, complications, and simultaneous infection. We report a patient who developed severe GBS following SARS-CoV-2 infection at the peak of the initial COVID-19 surge (April 2020) in New York City and discuss diagnostic and management issues and complications that may warrant special consideration in similar patients.
People living with HIV have high rates of anal human papillomavirus infection and anal precancer/cancer.
This study aims to: 1) determine human papillomavirus subtype distribution among people living ...with HIV with anal high-grade squamous intraepithelial lesions; 2) compare the clinicopathological characteristics of patients with anal high-grade squamous intraepithelial lesions by human papillomavirus 16 status; and 3) investigate high-risk human papillomavirus negative anal high-grade squamous intraepithelial lesion cases.
In this retrospective study, 700 people living with HIV who have biopsy-proven anal high-grade squamous intraepithelial lesions were reviewed for demographics, cytological diagnoses, and human papillomavirus testing results for human papillomavirus 16, 18, and 12 other high-risk types. For human papillomavirus-negative subjects, corresponding biopsies were genotyped by using real-time polymerase chain reaction.
This study was conducted in a large urban HIV clinic system and major referral center for anal cancer screening.
Median age was 46 years (range, 20-76). Ninety-one percent of the patients were men who have sex with men.
The primary outcome measure was the association between demographic variables and human papillomavirus 16 status.
Anal cytology was unsatisfactory (5%), benign (13%), atypical squamous cells of undetermined significance (35%), low-grade squamous intraepithelial lesion (36%), and high-grade squamous intraepithelial lesions (11%). Human papillomavirus cotesting results were negative (n = 38, 5%), human papillomavirus 16 (n = 303, 43%), human papillomavirus 18 (n = 78, 11%), or exclusively non-16/18 types (n = 281, 40%). Human papillomavirus 16 positivity was associated with ≥3 high-grade lesions and ≥ low-grade squamous intraepithelial lesion cytology (p < 0.001). Age, race/ethnicity, sex, smoking, CD4+ T-cell count, and HIV viral load did not differ by status of human papillomavirus 16 (p > 0.05). For human papillomavirus-negative cases, human papillomavirus genotyping of biopsies was positive for high-risk (n = 14, 36%) or possibly carcinogenic types (n = 12, 32%), or negative (n = 12, 32%).
This was a retrospective data analysis, and it pooled the results for 12 high-risk human papillomavirus types rather than individual types.
Nearly all people living with HIV and anal high-grade squamous intraepithelial lesions test positive for high-risk human papillomavirus on anal swabs; negative results may be due to sampling error, L1-based polymerase chain reaction assay, or human papillomavirus types not captured by standard clinical assays. Patients who have human papillomavirus 16-positive anal high-grade squamous intraepithelial lesions are indistinguishable from others based on demographic and clinical characteristics, underscoring the potential role of human papillomavirus testing for anal cancer screening. See Video Abstract at http://links.lww.com/DCR/B208. PACIENTES PORTADORES DE VIH CON PRECURSORES DE CÁNCER DE ANO: CARACTERÍSTICAS CLINICOPATOLÓGICAS Y DISTRIBUCIÓN DEL SUBTIPO VPH: Los pacientes portadores de VIH tienen altas tasas de infección por VPH y alto riesgo de desarrolar lesiones precáncerosas / cáncerosas del ano.(1) Determinar la distribución del subtipo de VPH entre las personas portadoras de VIH con lesiones intraepiteliales escamosas anales de alto grado. (2) Comparar las características clinicopatológicas de pacientes con lesiones intraepiteliales escamosas anales de alto grado del subtipo VPH 16. (3) Investigar casos de lesiones intraepiteliales escamosas anales de alto grado negativas para el VPH de alto riesgo.Estudio retrospectivo sobre 700 personas portadoras de VIH con lesiones intraepiteliales escamosas anales de alto grado confirmadas por biopsia. Los datos fueron revisados para determinar información demográfica, diagnósticos citológicos y resultados de tipización en el VPH subtipos 16 y 18, y otros 12 tipos de alto riesgo. Para los individuos negativos al VPH, se analizó el genotipo en las biopsias correspondientes mediante test de PCR en tiempo real.Extenso sistema de clinicas urbanas tratando VIH y un importante centro de referencia para la detección del cáncer analla mediana de edad poblacional fue de 46 años (rango, 20-76). 91% eran hombres que tenían sexo con hombres.Asociación entre las variables demográficas y el estado del VPH subtipo16.la citología anal fue insatisfactoria (5%), benigna (13%), células escamosas atípicas de importancia indeterminada (35%), lesión intraepitelial escamosa de bajo grado (36%) y lesiones intraepiteliales escamosas de alto grado (11%). Los resultados de la prueba conjunta del VPH fueron negativos (n = 38, 5%), el virus del VPH subtipo 16 (n = 303, 43%), el VPH subtipo 18 (n = 78, 11%) o los subtipos exclusivamente no 16/18 (n = 281, 40%). La positividad del VPH subtipo 16 se encotraba asociado con ≥3 lesiones de alto grado y ≥ células escamosas atípicas en la prueba de citología de indeterminada importancia (p < 0.001). La edad, la raza / etnia, el sexo, el tabaquismo, el recuento de células T CD4 + y la carga viral del VIH no difirieron según el estado del VPH subtipo 16 (p > 0.05). Para los casos negativos al VPH, el genotipo del virus del papiloma humano de las biopsias fue positivo para los tipos de alto riesgo (n = 14, 36%) o posiblemente carcinogénicos (n = 12, 32%), o negativo (n = 12, 32%).Análisis de datos retrospectivos, con resultados agrupados para 12 tipos de VPH de alto riesgo en lugar de tipos individuales.Casi todas las personas portadoras de VIH con lesiones intraepiteliales escamosas anales de alto grado dan positivo para el VPH de alto riesgo al muestreo de hisopos anales; Los resultados negativos pueden deberse a un error en el muestreo y al análisis de PCR basado en L1 o subtipos de VPH no obtenidos en los ensayos clínicos estándar. Los pacientes con lesiones intraepiteliales escamosas anales de alto grado positivas para el VPH subtipo 16 no son identificables de los demás, en función de las características demográficas y clínicas, lo que minimiza el rol potencial de la prueba del VPH en la detección del cáncer anal. Consulte Video Resumen en http://links.lww.com/DCR/B208. (Traducción-Dr. Xavier Delgadillo).
Abstract
Objectives
As part of an active MRSA surveillance programme in our neonatal ICU, we identified nares surveillance cultures from two infants that displayed heterogeneity in methicillin ...resistance between isolated subclones that lacked mecA and mecC.
Methods
The underlying mechanism for the modified Staphylococcus aureus (MODSA) methicillin-resistance phenotype was investigated by WGS.
Results
Comparison of finished-quality genomes of four MODSA and four MSSA subclones demonstrated that the resistance changes were associated with unique truncating mutations in the gene encoding the cyclic diadenosine monophosphate phosphodiesterase enzyme GdpP or a non-synonymous substitution in the gene encoding PBP2.
Conclusions
These two cases highlight the difficulty in identifying non-mecA, non-mecC-mediated MRSA isolates in the clinical microbiology laboratory, which leads to difficulties in implementing appropriate therapy and infection control measures.
spp. cause serious invasive lung infections, and
is the most commonly encountered clinically significant species. Voriconazole is considered to be the drug of choice for treating
infections; however, ...rising resistance rates have been reported. We evaluated a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based method for the differentiation between wild-type and non-wild-type isolates of 20
spp. (including 2 isolates of
and 1 of
that were used as controls due their intrinsic low azole susceptibility with respect to the
response to voriconazole). At 30 and 48 h of incubation, there was complete agreement between Cyp51A sequence analysis, broth microdilution, and MALDI-TOF MS classification of isolates as wild type or non-wild type. In this proof-of-concept study, we demonstrated that MALDI-TOF MS can be used to accurately detect
strains with reduced voriconazole susceptibility. However, rather than proving to be a rapid and simple method for antifungal susceptibility testing, this particular MS-based method showed no benefit over conventional testing methods.
PDF
