Collect that Stool! The Impact of Delay in Specimen Collection to NHSN Lab ID C. difficile Events

Abstract Background The use of a remote specimen collection strategy employing a kit designed for unobserved self-collection for SARS-CoV-2 RT-PCR can decrease the use of PPE and exposure risk. To assess the impact of unobserved specimen self-collection on test performance, we examined results from a SARS-CoV-2 qualitative RT-PCR test for self-collected specimens from participants in a return-to-work screening program and assessed the impact of a pooled testing strategy in this cohort. Methods Self-collected anterior nasal swabs from employee return to work programs were tested using the Quest Diagnostics SARS-CoV-2 RT-PCR EUA. The Ct values for the N1 and N3 N-gene targets and a human RNase P (RP) gene control target were tabulated. For comparison, we utilized Ct values from a cohort of HCP-collected specimens from patients with and without COVID-19 symptoms. Results Among 47,923 participants, 1.8% were positive. RP failed to amplify for 13/115,435 (0.011%) specimens. The median (IQR) Cts were 32.7 (25.0-35.7) for N1 and 31.3 (23.8-34.2) for N3. Median Ct values in the self-collected cohort were significantly higher than those of symptomatic, but not asymptomatic patients. Based on Ct values, pooled testing with 4 specimens would have yielded inconclusive results in 67/1,268 (5.2%) specimens but only a single false-negative result. Conclusions Unobserved self-collection of nasal swabs provides adequate sampling for SARS-CoV-2 RT-PCR testing. These findings alleviate concerns of increased false negatives in this context. Specimen pooling could be used for this population as the likelihood of false negative results is very low due when using a sensitive, dual-target methodology.

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Herbarium specimens as tools to assess the impact of large herbivores on plant species

Botany ◽

10.1139/cjb-2016-0206 ◽

2017 ◽

Vol 95 (2) ◽

pp. 153-162 ◽

Cited By ~ 6

Author(s):

Marie-Pierre Beauvais ◽

Stéphanie Pellerin ◽

Jean Dubé ◽

Claude Lavoie

Keyword(s):

Leaf Area ◽

Plant Morphology ◽

Herbarium Specimens ◽

Large Herbivore ◽

Large Herbivores ◽

Environmental Pressures ◽

Specimen Collection ◽

Data Source ◽

Rich Data ◽

The Impact

Herbarium specimens can be used to reconstruct spatiotemporal changes in plant morphology caused by environmental pressures. The reliability of herbarium-derived data requires evaluation, because specimen collection is subject to biases. We used herbarium and field data to investigate the impact of large herbivore browsing on the size of a forb. White trillium (Trillium grandiflorum (Michaux) Salisbury) was studied because the impacts of white-tailed deer (Odocoileus virginianus Zimmermann) browsing on this species are well-known. A total of 692 herbarium specimens collected in Quebec (Canada) were used to evaluate leaf area. Leaf area values of herbarium specimens were compared with those of modern (2013, 2014) specimens collected in sites either with >8 deer per square kilometre or without deer. Flowering individuals in modern sites with deer had a significantly lower leaf area than herbarium specimens and modern specimens collected in sites without deer. The distribution of white trillium individuals in deer sites was also skewed towards plants with a smaller leaf area. Herbarium specimens may offer unique and inexpensive data, compared with methods traditionally used to assess the impacts of herbivores on plants, such as exclosures or clipping experiments. Unfortunately, this rich data source is seriously jeopardized by the downtrend in specimen collecting.

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Impact of a Rapid Herpes Simplex Virus PCR Assay on Duration of Acyclovir Therapy

Journal of Clinical Microbiology ◽

10.1128/jcm.02559-16 ◽

2017 ◽

Vol 55 (5) ◽

pp. 1557-1565 ◽

Cited By ~ 19

Author(s):

Tam T. Van ◽

Kanokporn Mongkolrattanothai ◽

Melissa Arevalo ◽

Maryann Lustestica ◽

Jennifer Dien Bard

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Signs And Symptoms ◽

Turnaround Time ◽

Pcr Assay ◽

Specimen Collection ◽

The Central Nervous System ◽

Acyclovir Therapy ◽

Simplex Virus ◽

The Impact

ABSTRACTHerpes simplex virus (HSV) infections of the central nervous system (CNS) are associated with significant morbidity and mortality rates in children. This study assessed the impact of a direct HSV (dHSV) PCR assay on the time to result reporting and the duration of acyclovir therapy for children with signs and symptoms of meningitis and encephalitis. A total of 363 patients with HSV PCR results from cerebrospinal fluid (CSF) samples were included in this retrospective analysis, divided into preimplementation and postimplementation groups. For the preimplementation group, CSF testing was performed using a laboratory-developed real-time PCR assay; for the postimplementation group, CSF samples were tested using a direct sample-to-answer assay. All CSF samples were negative for HSV. Over 60% of patients from both groups were prescribed acyclovir. The average HSV PCR test turnaround time for the postimplementation group was reduced by 14.5 h (23.6 h versus 9.1 h;P< 0.001). Furthermore, 79 patients (43.6%) in the postimplementation group had dHSV PCR results reported <4 h after specimen collection. The mean time from specimen collection to acyclovir discontinuation was 17.1 h shorter in the postimplementation group (31.1 h versus 14 h;P< 0.001). The median duration of acyclovir therapy was also significantly reduced in the postimplementation group (29.2 h versus 14.3 h;P= 0.01). Our investigation suggests that implementation of rapid HSV PCR testing can decrease turnaround times and the duration of unnecessary acyclovir therapy.

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Dual intervention with a lymph node (LN) specimen collection kit and enhanced specimen dissection to improve staging of resectable non-small cell lung cancer (NSCLC).

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.7569 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. 7569-7569

Author(s):

Srishti Sareen ◽

Robert A. Ramirez ◽

Ahmed Yasir Javed ◽

Laura Elizabeth Miller ◽

Christopher Wang ◽

...

Keyword(s):

Adjuvant Therapy ◽

Conditional Logistic Regression ◽

Extent Of Resection ◽

Nodal Staging ◽

Small Cell Lung ◽

Surgical Specimen ◽

Specimen Collection ◽

Advanced Planning ◽

Matched Case ◽

The Impact

7569 Background: LN metastasis impairs survival of resectable NSCLC, but routine pathologic nodal staging is suboptimal. We tested the impact of a dual intervention (a surgical specimen collection kit with specific, pre-labeled LN collection cups, to improve intraoperative hilar/mediastinal LN dissection; and a fastidious gross dissection of the resected lung specimen for perihilar/intrapulmonary LNs) on the rate of detection of LN metastasis. Methods: We matched dual intervention cases with controls performed with standard surgical specimen collection and pathology examination protocols. Controls were hierarchically matched for extent of resection, laterality, surgeon, pathologist and T-stage. All statistical comparisons were made with Exact Conditional Logistic Regression, to account for the matched case-control design. Results: Patient demographic, tumor histology, and size characteristics were similar between the groups. The impact of the dual interventions is shown in the Table. Conclusions: The dual interventions significantly increased retrieval of N1 and N2 LNs, the rate of detection of LN metastasis, and nodal up-staging. There were strong trends towards higher aggregate stage and increased adjuvant therapy eligibility. The interventions may improve stage-adjusted survival by improving stage accuracy, and improve aggregate survival by increasing the appropriate use of post-operative adjuvant therapy. A prospective randomized trial to test survival impact of the dual interventions is at an advanced planning phase. [Table: see text]

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Influence of Antibiotics on the Detection of Bacteria by Culture-Based and Culture-Independent Diagnostic Tests in Patients Hospitalized With Community-Acquired Pneumonia

Open Forum Infectious Diseases ◽

10.1093/ofid/ofx014 ◽

2017 ◽

Vol 4 (1) ◽

Cited By ~ 18

Author(s):

Aaron M. Harris ◽

Anna M. Bramley ◽

Seema Jain ◽

Sandra R. Arnold ◽

Krow Ampofo ◽

...

Keyword(s):

Legionella Pneumophila ◽

Diagnostic Tests ◽

Chlamydia Pneumoniae ◽

Community Acquired Pneumonia ◽

Blood Cultures ◽

Antibiotic Administration ◽

Antibiotic Exposure ◽

Specimen Collection ◽

Culture Independent ◽

The Impact

Abstract Background Specimens collected after antibiotic exposure may reduce culture-based bacterial detections. The impact on culture-independent diagnostic tests is unclear. We assessed the effect of antibiotic exposure on both of these test results among patients hospitalized with community-acquired pneumonia (CAP). Methods Culture-based bacterial testing included blood cultures and high-quality sputum or endotracheal tube (ET) aspirates; culture-independent testing included urinary antigen testing (adults) for Streptococcus pneumoniae and Legionella pneumophila and polymerase chain reaction (PCR) on nasopharyngeal and oropharyngeal (NP/OP) swabs for Mycoplasma pneumoniae and Chlamydia pneumoniae. The proportion of bacterial detections was compared between specimens collected before and after either any antibiotic exposure (prehospital and/or inpatient) or only prehospital antibiotics and increasing time after initiation of inpatient antibiotics. Results Of 4678 CAP patients, 4383 (94%) received antibiotics: 3712 (85%) only inpatient, 642 (15%) both inpatient and prehospital, and 29 (<1%) only prehospital. There were more bacterial detections in specimens collected before antibiotics for blood cultures (5.2% vs 2.6%; P < .01) and sputum/ET cultures (50.0% vs 26.8%; P < .01) but not urine antigen (7.0% vs 5.7%; P = .53) or NP/OP PCR (6.7% vs 5.4%; P = .31). For all diagnostic testing, bacterial detections declined with increasing time between inpatient antibiotic administration and specimen collection. Conclusions Bacteria were less frequently detected in culture-based tests collected after antibiotics and in culture-independent tests that had longer intervals between antibiotic exposure and specimen collection. Bacterial yield could improve if specimens were collected promptly, preferably before antibiotics, providing data for improved antibiotic selection.

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Comparison of three nasopharyngeal swab types and the impact of physiochemical properties for optimal SARS-CoV-2 detection

10.1101/2020.10.21.20206078 ◽

2020 ◽

Author(s):

Trish R. Kahamba ◽

Lara Noble ◽

Wendy Stevens ◽

Lesley Scott

Keyword(s):

Clinical Diagnostics ◽

Automated System ◽

Molecular Diagnostic ◽

Medical Apparatus ◽

Specimen Collection ◽

Sterile Phosphate Buffer ◽

Significant Difference ◽

The Impact

AbstractAdequate swab specimen collection, release and detection of nucleic acids by molecular diagnostic assays is largely attributed to the physical and chemical characteristics of different swab types. We investigated properties of three types of commercial nasopharyngeal swabs (nylon flocked: Type 1-Media Merge; Type 2-Kang Jian Medical Apparatus, China and Type 3-Wuxi NEST Biotechnology Co. Ltd, China) used in clinical diagnostics with the aim to establish if different swab designs and configurations had any effect on swab performance. Properties investigated included viral absorption, release, capture, extraction and recovery efficiency from each swab for the detection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). All swab types (n=18) were inoculated with different amounts of SARS-CoV-2 live viral cultures (1:10, 1:100 and 1:1000 copies/ml) and eluted in sterile phosphate buffer saline. RNA was extracted from all swab eluates using a fully automated system (BD MAX™ System) and cycle threshold (Ct) values were compared. RNA stability was also investigated after dry storage of swabs at room temperature for 72 hours. Statistically significant differences (p<0.05) were observed in the absorption and release capabilities between Type 1 and 3 as well as between Type 2 and 3 swabs, however, no significant difference was observed between Type 1 and 2. Ct values and extraction efficiency amounts of SARS-CoV-2 varied amongst the swab types. We conclude that in order to facilitate accurate SARS-CoV-2 diagnosis, assessment of NP swab characteristics is of importance before implementation for specimen collection in the clinical setting.

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Deep ocean seascape and Pseudotanaidae (Crustacea: Tanaidacea) diversity at the Clarion-Clipperton Fracture Zone

Scientific Reports ◽

10.1038/s41598-019-51434-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Aleksandra Jakiel ◽

Ferran Palero ◽

Magdalena Błażewicz

Keyword(s):

Deep Sea ◽

Deep Ocean ◽

Genetic Data ◽

Tropical Eastern Pacific ◽

Benthic Species ◽

Specimen Collection ◽

Clipperton Fracture Zone ◽

Limited Dispersal ◽

Clarion Clipperton Fracture Zone ◽

The Impact

AbstractUnderstanding the diversity and spatial distribution of benthic species is fundamental to properly assess the impact of deep sea mining. Tanaidacea provide an exceptional opportunity for assessing spatial patterns in the deep-sea, given their low mobility and limited dispersal potential. The diversity and distribution of pseudotanaid species is characterized here for the Clarion and Clipperton Fractures Zone (CCZ), which is the most extensive deposit field of metallic nodules. Samples were taken from the Belgian, German and French license areas, but also from the APEI 3 (Area of Particular Environmental Interest 3) of the Interoceanmetal consortium associates. The combination of morphological and genetic data uncovered one new pseudotanaid genus (Beksitanais n. gen.) and 14 new species of Pseudotanais (2 of them virtual taxa). Moreover, our results suggest that spatial structuring of pseudotanaid diversity is correlated with deep-sea features, particularly the presence of fractures and seamount chains crossing the CCZ. The presence of geographical barriers delimiting species distributions has important implications for the establishment of protected areas, and the APEI3 protected area contains only one third of the total pseudotanaid species in CCZ. The specimen collection studied here is extremely valuable and represents an important first step in characterizing the diversity and distribution of pseudotanaids within the Tropical Eastern Pacific.

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Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis

10.1101/2020.11.12.20230748 ◽

2020 ◽

Cited By ~ 1

Author(s):

Rose A. Lee ◽

Joshua C. Herigon ◽

Andrea Benedetti ◽

Nira R. Pollock ◽

Claudia M. Denkinger

Keyword(s):

Meta Analysis ◽

Diagnostic Testing ◽

Rna Extraction ◽

High Sensitivity ◽

Nucleic Acid Amplification ◽

Sample Collection ◽

Specimen Collection ◽

Nasal Swabs ◽

The Impact ◽

Alternative Specimen

ABSTRACTBackgroundNasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs.MethodsWe systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias.ResultsFrom 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (0.82, 95% CI: 0.73-0.90), OP (0.84, 95% CI: 0.57-1.0), saliva (0.88, 95% CI: 0.81 – 0.93)] than NP swabs, while combined OP/NS matched NP performance (0.97, 95% CI: 0.90-1.0). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield.ConclusionsNP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to head studies of sampling strategies are urgently needed.

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Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis

Journal of Clinical Microbiology ◽

10.1128/jcm.02881-20 ◽

2021 ◽

Cited By ~ 1

Author(s):

Rose A. Lee ◽

Joshua C. Herigon ◽

Andrea Benedetti ◽

Nira R. Pollock ◽

Claudia M. Denkinger

Keyword(s):

Meta Analysis ◽

Diagnostic Testing ◽

Rna Extraction ◽

High Sensitivity ◽

Nucleic Acid Amplification ◽

Sample Collection ◽

Specimen Collection ◽

Nasal Swabs ◽

The Impact ◽

Alternative Specimen

Background: Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. Methods: We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias. Results: From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (82%, 95% CI: 73-90%), OP (84%, 95% CI: 57-100%), saliva (88%, 95% CI: 81 – 93%)] than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90-100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield. Conclusions: NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to head studies of sampling strategies are urgently needed.

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Formation of Lunar Craters and Bright Rays as a Result of Meteorite Impacts

Symposium - International Astronomical Union ◽

10.1017/s0074180900178404 ◽

1962 ◽

Vol 14 ◽

pp. 415-418

Author(s):

K. P. Stanyukovich ◽

V. A. Bronshten

Keyword(s):

Explosive Charge ◽

The Moon ◽

Meteorite Impacts ◽

The Earth ◽

Lunar Craters ◽

The Impact

The phenomena accompanying the impact of large meteorites on the surface of the Moon or of the Earth can be examined on the basis of the theory of explosive phenomena if we assume that, instead of an exploding meteorite moving inside the rock, we have an explosive charge (equivalent in energy), situated at a certain distance under the surface.

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