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251 results for “Swabs”
Human papillomavirus (HPV) detection in vaginal self-samples: evaluation of eNat® as an alternative suspension medium to ThinPrep®PreservCyt® for vaginal swabs
<p>Dataset 1: HPV positivity on cervical and vaginal self-samples with different HPV real-time PCR assays</p> <p>Dataset 2: hrHPV viral load in cervical and vaginal self-samples</p> <p>Datakey 1: HPV positivity on cervical and vaginal self-samples with different HPV real-time PCR assays</p> <p>Datakey 2: hrHPV viral load in cervical and vaginal self-samples</p>
Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
<p>Genetic research is a key component to modern wildlife conservation, but it is contingent on the collection of reliable and high-quality genetic samples. Invasive genetic sampling techniques have potential to negatively impact individuals, which may be prohibitive when working with threatened and endangered species. Prior to sample collection, project managers must try to balance the negative impact on individuals included in the study with the demand for DNA and the difficulty of obtaining samples. Although established methods for blood and tissue collection in reptiles meet the need for high-quantity and quality DNA, they inherently require longer handling times and more skill to obtain. Thus, non-invasive DNA collection methods, such as cloacal swabs, may be preferred when animal welfare is a priority. Cloacal swabs are quicker, easier, require less training and reduce handling time. To evaluate cloacal swabbing as an alternative to collecting blood, we obtained both cloacal and blood swabs. We extracted DNA from cloacal and blood cells that were collected from 23 Timber Rattlesnakes (Crotalus horridus). We assessed DNA by purity (A260/A280), concentration, and microsatellite genotyping. Our results show high-quality DNA can be obtained from both cloacal swabs and blood samples, but quality and concentration of DNA was significantly lower from cloacal swabs. Further, degradation and contamination affects the performance of cloacal DNA when compared to blood DNA in microsatellite-based genotyping. Although we recommend collecting blood samples whenever possible to obtain the highest-quality DNA, cloacal swabs represent a viable alternative for genetic sampling when using microsatellite loci as genetic markers.</p>
Fig. 2 in A novel quantitative real-time PCR diagnostic assay for fecal and nasal swab detection of an otariid lungworm, Parafilaroides decorus
Fig. 2. Standard curve based on sensitivity data. A 95% confidence interval for the linear regression model is shaded in grey.
Fig. 1. Repeat family selection for the P. decorus diagnostic assay. A in A novel quantitative real-time PCR diagnostic assay for fecal and nasal swab detection of an otariid lungworm, Parafilaroides decorus
Fig. 1. Repeat family selection for the P. decorus diagnostic assay. A. Number of sequencing reads for P. decorus compared to outgroup species reads for each repeat family (1–104) on a log scale. Arrows indicate repeat families with no reads from the outgroup species. Plot was made using Tableau Software, 2019. B. Within a cluster, reads with similar sequences are closer together. Edges connect a read with its closest match (creating a pair) and the length of this edge represents the amount of overlap between the reads. The mean edge width provides context for the lengths in the cluster, so in a cluster with a larger mean edge width the edges are actually longer than edges in a cluster with a smaller mean edge width. Reads therefore may be distant because of sequence divergence, or in the case of a long repeat (more than 150 base pairs), because of a lack of overlap between reads. However, because there will likely be continuous reads covering different regions of the repeat, these longer repeats should still appear as a tight, though possibly larger, cluster. Read dots that stray from the central cluster most likely represent sequence divergence. Higher density therefore indicates lower sequence divergence.
Fig. S1. Toad skin swab cultures. Culture plates from A in Comparison of in vitro methods to inhibit growth of a virulent strain of Batrachochytrium dendrobatidis (Longcore, Pessier, and Nichols 1999)
Fig. S1. Toad skin swab cultures. Culture plates from A. boreas skin swabs after three days incubation at 25 °C.
Proteomic and metabolomic analysis of COVID-19 nasal swabs
<p>The epithelial barrier's primary role is to protect against entry of foreign and pathogenic elements. Global and targeted approaches were applied to nasal swabs from healthy and COVID-19-confirmed cases within 24 hours post-positive-confirmation and at 3 weeks post-infection to observe changes in proteome and metabolome.</p> <p>We found that the tryptophan/kynurenine metabolism pathway is a pinch-point regulator of canonical and non-canonical transcription activation, macrophage release of cytokines and significant changes in the immune and metabolic status with increasing severity and disease course.</p>
Swab Testing to Optimize Pneumonia Treatment with Empiric Vancomycin
ClinicalTrials.gov study NCT06272994. IPD Sharing: YES. Countries: 1. Publications: 24.
Proteomic and metabolomic analysis of COVID-19 nasal swabs
Open the record for dataset details and reuse information.
Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
Open the record for dataset details and reuse information.
A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs.
<p>The spectra were provided as unprocessed raw data in the manufacturers data format (Bruker), as labelled two zip archives with SARS CoV 2 positives and negative, according to the reviewer's recommendation.</p> <p>This information belongs to the publication (in review in <em>Journal of Virological Methods</em>)<br> "A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs"<br> All the information belongs to the National Reference Institute, INEI-ANLIS DR CARLOS G MALBRAN, BUENOS AIRES, ARGENTINA.</p>
Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and feces
<p>Microbial diversity and community function are related, and both can be highly specialized in different regions of the gut. The cloacal microbiome of Sceloporus virgatus lizards has low diversity, suggesting a specialized function, and is known to transfer antifungal microbes to eggshells during oviposition. We hypothesize that the cloacal microbiome is distinct from other parts of the digestive and reproductive systems. Here, we compare the microbiome of tissue samples from the cloaca, lower intestine, upper intestine, and oviduct. We further assessed whether common methods of microbial sampling – cloacal swabs and feces – provide accurate representations of these tissues, and whether feces might "seed" the cloacal microbiome. We found that the upper intestine and oviduct had unique microbial communities, while the lower intestine and cloaca had similar communities with lower diversity indicative of regional specialization. The cloacal community, in particular, showed extreme specialization averaging 99% Proteobacteria (Phylum) and 83% Enterobacteriacaea (Family). Cloacal swabs recovered communities similar to that of lower intestine and cloacal tissues, but fecal samples had much higher diversity and a distinct composition (62% Firmicutes and 39% Lachnospiraceae) relative to all gut regions. This result serves as a caution against the frequent assumption that fecal samples provide an accurate representation of the gut. Finally, we found that defecation did not alter the cloacal microbiome, suggesting that community is robust to perturbations from transient microbiota. </p>
Data from: Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs
<p>The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of Single Nucleotide Polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics' Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10ng of host DNA (ATG's recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 86.7% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 03
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 03 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). One infected ciliated cell is visible in the center of the recorded area. Virus particles are visible within membrane-bound compartments of the cytoplasm. Spike visibility is poor and some virus particles appear compressed.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 04
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 04 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (negative control). The recorded area shows the profiles of four keratinocytes which are surrounded by heterogenous material (e.g. membrane lamella, needle-like crystals, round profiles with a fine-fibrous matrix). Virus partricles are not visible.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 01
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 01 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). Two, more or less, intact ciliated cells are visible and surrounded by other cells or cellular debris. The ciliated cell in the upper right corner is infected with SARS-CoV-2. Virus particles are visible within membrane-bound compartments of the cytoplasm. Several double-membrane vesicles, which are typical compartments of the coronavirus replication machinery, are also detectable.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 02
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 02 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). One ciliated cell is visible and surrounded by cellular debris. The ciliated cell is infected with SARS-CoV-2. Few virus particles are visible within membrane-bound compartments of the cytoplasm. Numerous virus particles are located at the cell surface intermingled between the cilia. The virus particles of this cell appear deformed and deviate from the oval/circular profile which is usually present.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 07
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 07 comprises three stitched image montages recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (control). Ciliated cells and extracellular material, such as vesicles and needle-like crystals, are visible, but no coronavirus particles.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 06
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 06 comprises three stitched image montages recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (control). Ciliated cells and extracellular material, such as vesicles and needle-like crystals, are visible, but no coronavirus particles.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Assessing the prevalence of Female Genital Schistosomiasis and comparing the acceptability and performance of health worker-collected and self-collected cervical-vaginal swabs using PCR testing among women in North-Western Tanzania: the ShWAB study
<p>Female genital schistosomiasis (FGS) is a severe neglected disease, caused by infection with <em>Schistosoma haematobium</em>. The WHO has prioritized the improvement of diagnostics for FGS and previous studies have explored the PCR-based detection of <em>Schistosoma</em> DNA on genital specimens, with encouraging results. We aimed to determine the prevalence of FGS among women living in an endemic district in North-western Tanzania, applying and preliminary comparing self-collected and operator-collected cervical-vaginal swabs followed by PCR, and to assess the acceptability of these sampling procedures.</p>
Data from: A comparison of non-destructive visceral swab and tissue biopsy sampling methods for genotyping-by-sequencing in the freshwater mussel Fusconaia askewi
<p>Limiting harm to organisms via genetic sampling is an important consideration for rare species. Nondestructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the Unionid freshwater mussel, Texas Pigtoe (<em>Fusconaia askewi</em>). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared to swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence) while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.</p>
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International Brain Laboratory public data
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OpenNeuro
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