The Extraction and Recovery Efficiency of Pure <scp>DNA</scp> for Different Types of Swabs

Bruijns, Brigitte; Tiggelaar, Roald M.; Gardeniers, Han

doi:10.1111/1556-4029.13837

Cited by 90 publications

(112 citation statements)

References 22 publications

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“…This was despite studies indicating that cotton swabs could trap (i.e. not release) some of the biological material collected or could interact with the DNA extraction process, resulting in a loss of material for the DNA analysis [13,21,22]. In addition, published research has shown different DNA yield because of swab models variable performance [11].…”

Section: Discussionmentioning

confidence: 99%

“…This may be because of the complex nature of touch DNA, which consists mostly of sloughed, enucleated keratinocytes [23,24] and extracellular [25], partially degraded DNA derived from apoptotic epithelial cells, sebaceous [26] or sweat glands [27]. For this reason, it is complicated to identify which of the following variables (or their combinations) have a significant influence on DNA collection [1,21,[28][29][30]: the swab head size, the layout and type of fibers, the static electricity of a dry swab, the use of a solvent to moisten the swab and consequently the substrate, the operator or the drying system. In the first part of this study, the relative and global performance as well as the practicality of four swabs considered for collecting touch DNA on three different substrates was assessed.…”

Section: Discussionmentioning

confidence: 99%

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Touch DNA collection – Performance of four different swabs

Comte

Baechler

Gervaix

et al. 2019

Forensic Science International: Genetics

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A collaborative study conducted by three police forensic units, a DNA laboratory, and a forensic academic institute was undertaken in order to compare the performance of four different swabs in controlled and quasioperational conditions. For this purpose, a reference swab (Prionics cardboard evidence collection kit) currently used within the police forensic units and 3 challenger swabs (COPAN 4N6FLOQSwabs™ (Genetics variety), Puritan FAB-MINI-AP and Sarstedt Forensic Swab) were used for collecting DNA traces from previously used items (referred as "touch DNA" in this article) including on 60 collars, 60 screwdrivers and 60 steering wheels obtained from volunteers. For each comparison, the surface considered was divided into two equal components; one was sampled with the reference swab and the other with one of the three challenger swabs. This lead to a total of 360 samples. Conclusions were consistent within the four operational partners. From a practical point of view, the COPAN 4N6FLOQSwabs™ (Genetics variety) was judged the most convenient to use. Furthermore, it allowed the recovery of significantly more DNA from collars (0.65 vs 0.13 ng/μL) and steering wheels (2.82 vs 1.77 ng/μL), and a similar amount of DNA from screwdrivers (0.032 vs 0.026 ng/μL) compared with the Prionics reference swab. The two other challenger swabs provided results that were not significantly different from the reference swab, except for the Puritan swab, whose performance was significantly lower for steering wheels (0.37 vs 0.58 ng/μL). As part of a conservation study, 50 μL of a blood dilution (1/4 with PBS) was deposited on a total of 105 COPAN (Genetics and Crime Scene varieties), Prionics and Sarstedt swabs. They were stored within a cupboard at room temperature. The integrity of the recovered DNA was evaluated with NGM SElect™ DNA profiles after different time-spans ranging from 1 day to 12 months by comparing the height difference of the peaks occurring at the shortest and longest loci, respectively. DNA seemed to remain stable, except when using the COPAN 4N6FLOQSwabs™ treated with an antimicrobial agent (Crime scene variety), which resulted in significant DNA degradation. Following these tests, the COPAN 4N6FLOQSwabs™ (Genetics variety), a model with a desiccant, was selected for further testing in fully operational conditions.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Touch DNA collection – Performance of four different swabs

Comte

Baechler

Gervaix

et al. 2019

Forensic Science International: Genetics

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“…They found that cotton-tipped swabs were comparable to rayon-tipped swabs in obtaining the nasopharyngeal specimens needed to detect SARS-CoV-2 in 44 adults (19). However, polyester swabs were shown to have a larger absorption capacity and extraction efficiency, compared to cotton or rayon, in recovering human DNA from salivary samples (10).…”

Section: Downloaded Frommentioning

confidence: 99%

“…Polyester was chosen, as it was cheap and easy to source. Polyester has also been shown to be non-toxic to viral viability in transport media and is commonly used by several commercial swab manufacturers (10).…”

Section: Introductionmentioning

confidence: 99%

Low-Cost Polyester-Tipped Three-Dimensionally Printed Nasopharyngeal Swab for the Detection of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2)

et al. 2020

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Case identification, isolation and contact tracing are fundamental strategies used to control the spread of Coronavirus Disease 2019 (COVID-19). This has led to widespread testing that resulted in the interruption of the supply chain for testing materials around the world. A prospective study was conducted to compare cheap and easily sourced 3-dimensionally printed polylactic acid and polyester nasopharyngeal swabs to commercially manufactured swabs, in detecting severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). During the study period, 287 laboratory-confirmed hospitalized COVID-19 patients, at multiple stages of their illness, were enrolled. The median age for the study population was 47.6 years (IQR: 34.4-56.6 years) and two-thirds (67.6%) of the subjects were male. The median duration of hospitalization, at the time of sampling, was 13 days (IQR 10-16 days). Overall concordance between the prototype and control swabs was 80.8% (Cohen's kappa coefficient = 0.61). Most discrepant results were due to prototype-positive control-negative results. When considering all positive results to be true positives, the prototype swab had a higher sensitivity (90.6% vs 80.8%, 95%CI 85.7-94.0% and 74.7-85.7%, respectively, p < 0.015). The cost to produce the prototype swab was estimated to be 0.05 USD per swab. Polylactic acid 3D-printed polyester-tipped swabs were shown to be effective for nasopharyngeal sample collection. We believe that this design can easily be adopted in countries where commercial swabs are not readily available and can play a vital role in public health efforts for disease control in low-income countries.

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“…PCR-based techniques, especially quantitative (qPCR) have been widely used to quantify P. gingivalis DNA in saliva, dental plaque and other samples [7]. Most of these assays require DNA extraction or release processes which are not only time-consuming, but also result in loss of template DNA [8].…”

mentioning

confidence: 99%

An evaluation of direct PCR assays for the detection and quantification of Porphyromonas gingivalis

Kong

et al. 2020

Epidemiol. Infect.

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Porphyromonas gingivalis has been linked to the development and progression of oesophageal squamous cell carcinoma (ESCC), and is considered to be a high-risk factor for ESCC. Currently, the commonly used methods for P. gingivalis detection are culture or DNA extraction-based, which are either time and labour intensive especially for high-throughput applications. We aimed to establish and evaluate a rapid and sensitive direct quantitative polymerase chain reaction (qPCR) protocol for the detection of P. gingivalis without DNA extraction which is suitable for large-scale epidemiological studies. Paired gingival swab samples from 192 subjects undergoing general medical examinations were analysed using two direct and one extraction-based qPCR assays for P. gingivalis. Tris-EDTA buffer-based direct qPCR (TE-direct qPCR), lysis-based direct qPCR (lysis-direct qPCR) and DNA extraction-based qPCR (kit-qPCR) were used, respectively, in 192, 132 and 60 of these samples for quantification of P. gingivalis. The sensitivity and specificity of TE-direct qPCR was 95.24% and 100% compared with lysis-direct qPCR, which was 100% and 97.30% when compared with kit-qPCR; TE-direct qPCR had an almost perfect agreement with lysis-direct qPCR (κ = 0.954) and kit-qPCR (κ = 0.965). Moreover, the assay time used for TE-direct qPCR was 1.5 h. In conclusion, the TE-direct qPCR assay is a simple and efficient method for the quantification of oral P. gingivalis and showed high sensitivity and specificity compared with routine qPCR.

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The Extraction and Recovery Efficiency of Pure DNA for Different Types of Swabs

Cited by 90 publications

References 22 publications

Touch DNA collection – Performance of four different swabs

Touch DNA collection – Performance of four different swabs

Low-Cost Polyester-Tipped Three-Dimensionally Printed Nasopharyngeal Swab for the Detection of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2)

An evaluation of direct PCR assays for the detection and quantification of Porphyromonas gingivalis

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