Swab Types Research Articles

Oral Microbiome Analysis in Prospective Genome Cohort Studies of the Tohoku Medical Megabank Project.

A baseline oral microbiome study of the Tohoku Medical Megabank Organization (TMM) was planned to characterize the profile of the oral microbiome in the Japanese population. The study also aimed to clarify risk factors for multifactorial diseases by integrated analysis of the oral microbiome and host genome/omics information. From 2013 to 2016, we collected three types of oral biospecimens, saliva, supragingival plaque, and tongue swab, from a total of 25,101 participants who had a dental examination in TMM. In this study, we used two independent cohorts; the Community-Based Cohort and Birth and Three-Generation Cohort as discovery and validation cohorts, respectively, and we selected participants examined by a single dentist. We found through the 16S ribosomal RNA gene sequencing analysis of 834 participants of the Community-Based Cohort Study that there are differences in the microbial composition and community structure between saliva and plaque. The species diversities in both saliva and plaque were increased in correlation with the severity of periodontal disease. These results were nicely reproduced in the analysis of 455 participants of the Birth and Three-Generation Cohort Study. In addition, strong positive and negative associations of microbial taxa in both plaque and saliva with periodontitis-associated biofilm formation were detected by co-occurrence network analysis. The classes Actinobacteria and Bacilli, including oral health-associated bacterial species, showed a positive correlation in saliva. These results revealed differences in microbial composition and community structure between saliva and plaque and a correlation between microbial species and the severity of periodontal disease. We expect that the large database of the oral microbiome in the TMM biobank will help in the discovery of novel targets for the treatment and prevention of oral diseases, as well as for the discovery of therapeutic and/or preventive targets of systemic diseases.

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

BackgroundDetermining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a synthetic swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, synthetic, and foam) and one clinical-grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients including COVID-19+ patients. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent.ResultsCompared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2–4× higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved synthetic (SYN) swab. The limit of detection (LoD) of SARS-CoV-2 from floor samples collected using the consumer-grade plastic (CGp) or research-grade plastic The Microsetta Initiative (TMI) swabs was similar or better than the SYN swab, further suggesting that swab type does not impact RNA recovery as measured by the abundance of SARS-CoV-2. The LoD for TMI was between 0 and 362.5 viral particles, while SYN and CGp were both between 725 and 1450 particles. Lastly microbiome analyses (16S rRNA gene sequencing) of paired samples (nasal and floor from same patient room) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type, but instead driven by the patient and sample type.ConclusionsCompared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer-grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity and lack of antibiotics in these samples makes it possible to perform concomitant microbiome analyses.2qwatWsTfGwZ6-67p9eTYDVideo abstract

Variability in instructions for performance of nasopharyngeal swabs across Canada in the era of COVID-19 \u2013 what type of swab is actually being performed?

BackgroundThe primary method of surveillance for the presence of SARS-CoV-2 is with nasopharyngeal swabs. Given the significant demand for nasopharyngeal swabs, a large number of previously untrained and unfamiliar staff are now performing this test. It was noted that there was significant heterogeneity in instructions for performing nasopharyngeal swabs in Canada, in contrast to the guidance provided by the Centers for Disease Control and Prevention (CDC), and the Pan American Health Organization (PAHO). The objective of this study was to review the instructions provided across Canada and contrast them to those of the CDC and PAHO.MethodsA standard series of steps for nasopharyngeal swab performance was outlined based on the CDC, PAHO, and New England Journal of Medicine instructions. A comprehensive search was performed in August 2020 to identify nasopharyngeal swab guidelines provided by public health in the provinces and territories of Canada. Regional health authority guidance was also collected. Instructions provided were contrasted against the standardized steps.ResultsInstructions were identified for all provinces and territories, and for 81 regional health authorities. From the provincial and territorial guidelines, 10/13 (77%) cleared the nasal passages before swab insertion, 11/13 (85%) tilted the patient’s head back slightly, 12/13 (92%) inserted the swab parallel to the palate, but only 3/13 (23%) inserted the swab to at least a depth of two-thirds the distance between the patient’s nose and ear. A clear majority (81%) of regional health authority guidelines followed their respective provincial guidelines.For depth of insertion, Quebec provided a pictogram but no distance or technique for estimation. Six provinces and territories - Northwest Territories, Nunavut, Ontario, Saskatchewan, Prince Edward Island and Alberta - recommended 4 cm or one-half the distance from nostrils to ear. British Columbia and Manitoba recommended a 7 cm depth of insertion. Nova Scotia recommended one-half to two-thirds the distance from nose to ear. Lastly, Newfoundland, New Brunswick and the Yukon recommended an insertion from nose to the external ear canal.ConclusionThere is significant heterogeneity in guidance for nasopharyngeal swab performance across Canada. The instructions provided by the majority of provinces and territories in Canada would not be effective in reaching the nasopharynx.Graphical abstract

Routes and types of microbial infection in the pathology of pancreatic adenocarcinoma

Introduction/Objective. Pancreatic cancer may be accompanied by infections caused by various microorganisms. It is uncertain wheatear pancreatic infection precedes the development of cancer or vice versa. The aim of this study is to analyze routes of infections from the duodenum through the pancreatic duct to determine what types of microorganisms can get through this duct into the pancreas and nearby tissue. Methods. In patients subjected to cephalic duodenopancreatectomy (Whipple procedure) due to adenocarcinoma of the ampulla of Vater, the duodenum or head of the pancreas, swabs from duodenal mucosa, pancreatic duct, and pancreatic tissue at the line of the resection were taken. Microscopic slides were prepared directly from the patients? specimens as well as from colonies on culture plates, and both were Gram stained. Results. Candida was present in all three types of swabs (duodenum, pancreatic duct, and tissue), while bacteria, depending on the species (Pseudomonas aeruginosa, ?-hemolytic Streptococcus, coagulasenegative Staphylococcus, Enterococcus spp., Serratia spp.), were present in pancreatic duct or tissue, but not in the duodenum. Conclusion. There is a connection between the presence of microorganisms and pathology of the pancreatic adenocarcinoma. Results show that Candida infection originates from the duodenum, while bacterial infections originate directly from blood or tissue injuries.

A comparison of swab types on sample adequacy, suspects comfort and provider preference in COVID-19

AimThis study was aimed to compare the virological, suspect reported outcomes and provider preferences during COVID-19 swab taking procedure used for sampling. MethodsThe COVID-19 suspects are subjected to nasopharyngeal (NP) and oropharyngeal (OP) swabs for testing. Two types of swabs (Nylon and Dacron) are used for sample collection. Prospectively each suspect's response is collected and assessed for self-reported comfort level. The provider's experience with each suspect and virological outcomes recorded separately. The sample adequacy was compared based on swab types and demographic characteristics. ResultsA total of 1008 COVID-19 suspects were considered for comparison of various outcomes. Dacron and flocked Nylon swab sticks are used for taking 530 and 478 samples, respectively. Suspects who underwent the procedure using Nylon swabs were six times more likely to have pain/discomfort compared to when Dacron swab was used (Adj RR (95% CI: 6.76 (3.53 to 13, p=0.0001))). The providers perceived six times more resistance with the Nylon swabs compared to Dacron Swabs (Adj RR (95% CI: 5.96 (3.88 to 9.14, p=0.0001))). The pediatric population had a higher rate of blood staining in Dacron swab [Dacron 66 (80.5%); Nylon 51 (54.8%) p=0.0001]. The sample adequacy rate and laboratory positivity rate were not significantly different from each other. ConclusionsGiven the comparable virological outcomes, the difference in suspect and providers comfort should drive swab selection based on characteristics of the suspects. The bulbous Nylon swab caused more pain/discomfort in adults compared to Dacron.

Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR.

BackgroundReverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives are possible depending on swab type and time since symptom onset.AimTo determine how the probability of obtaining a false-negative test in infected patients is affected by time since symptom onset and swab type.MethodsWe used generalised additive mixed models to analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once.ResultsThe probability of a positive test decreased with time since symptom onset, with oropharyngeal (OP) samples less likely to yield a positive result than nasopharyngeal (NP) samples. The probability of incorrectly identifying an uninfected individual due to a false-negative test was considerably reduced if negative tests were repeated 24 hours later. For a small false-positive test probability (<0.5%), the true number of infected individuals was larger than the number of positive tests. For a higher false-positive test probability, the true number of infected individuals was smaller than the number of positive tests.ConclusionNP samples are more sensitive than OP samples. The later an infected individual is tested after symptom onset, the less likely they are to test positive. This has implications for identifying infected patients, contact tracing and discharging convalescing patients who are potentially still infectious.

Comparison of Three Nasopharyngeal Swab Types and the Impact of Physiochemical Properties for Optimal SARS-CoV-2 Detection

Adequate 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 dilution) 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.

Assessment of the direct quantitation of SARS-CoV-2 by droplet digital PCR

Droplet digital PCR (ddPCR) is a sensitive and reproducible technology widely used for quantitation of several viruses. The aim of this study was to evaluate the 2019-nCoV CDC ddPCR Triplex Probe Assay (BioRad) performance, comparing the direct quantitation of SARS-CoV-2 on nasopharyngeal swab with the procedure applied to the extracted RNA. Moreover, two widely used swab types were compared (UTM 3 mL and ESwab 1 mL, COPAN). A total of 50 nasopharyngeal swabs (n = 25 UTM 3 mL and n = 25 ESwab 1 mL) from SARS-CoV-2 patients, collected during the pandemic at IRCCS Sacro Cuore Don Calabria Hospital (Veneto Region, North-East Italy), were used for our purpose. After heat inactivation, an aliquot of swab medium was used for the direct quantitation. Then, we compared the direct method with the quantitation performed on the RNA purified from nasopharyngeal swab by automated extraction. We observed that the direct approach achieved generally equal RNA copies compared to the extracted RNA. The results with the direct quantitation were more accurate on ESwab with a sensitivity of 93.33% [95% CI, 68.05 to 99.83] and specificity of 100.00% for both N1 and N2. On the other hand, on UTM we observed a higher rate of discordant results for N1 and N2. The human internal amplification control (RPP30) showed 100% of both sensitivity and specificity independent of swabs and approaches. In conclusion, we described a direct quantitation of SARS-CoV-2 in nasopharyngeal swab. Our approach resulted in an efficient quantitation, without automated RNA extraction and purification. However, special care needs to be taken on the potential bias due to the conservation of samples and to the heating treatment, as we used thawed and heat inactivated material. Further studies on a larger cohort of samples are warranted to evaluate the clinical value of this direct approach.

Laboratory evaluation of the Sigma Transwab\xae transport system for the recovery of Candida species using the Clinical and Laboratory Standards Institute (CLSI) document M40-A2

Rising healthcare complications due to fungal infections increase the importance of efficient specimen collection and maintenance systems for correct identification and diagnosis. The CLSI M40-A2 protocol provides guidelines for laboratories assessing quality of medical transport devices, including swab transport systems (STS). This study assessed the efficiency of the Sigma Transwab® foam and flock swab in recovering and maintaining viability of different Candida spp. including C. auris, in different test conditions. Both swab types recovered and maintained viability of all Candida spp. with greater CFU at room temperature after incubation (24 and 48 h) in comparison with swabs maintained at 4 °C.

The novel use of a spray-on rubber coating to recover cellular material from the surface of bricks

Currently, forensic investigators utilise various types of swabs and tape lifts to recover cellular material from coarse surfaces identified during a criminal investigation. However, a number of challenges prevent successful recovery and therefore warrants the need for an alternative method. Plasti dip® is peel-off rubber coating that can be applied to most surfaces and may have an application in the recovery of DNA from coarse surfaces. The aim of this study was to determine the effectiveness of Plasti dip® to recover DNA from coarse brick surfaces and assess how this method compares to current techniques. Cellular material was deposited onto brick pieces in varying concentrations and recovered with either flocked, foam or rayon swabs, or Plasti dip®. Material recovered, using each technique, was extracted and quantitated for comparison of DNA yields. At low and medium cell concentrations, an observable but not statistically significant difference was observed between the swabbing methods and Plasti dip®. At high cell concentrations Plasti dip® was able to recover a significantly higher DNA concentration than all three swabbing methods. Quantitation results indicated no degradation of DNA. This is a novel approach to the collection of trace DNA from surfaces that have historically proven difficult to sample. While there is further validation required, this landmark study demonstrates the potential that spray-on rubber coatings have for casework involving rough, porous surfaces like bricks, stones or rocks.

Large-Scale, In-House Production of Viral Transport Media To Support SARS-CoV-2 PCR Testing in a Multihospital Health Care Network during the COVID-19 Pandemic.

The COVID-19 pandemic has severely disrupted worldwide supplies of viral transport media (VTM) due to widespread demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription-PCR (RT-PCR) testing. In response to this ongoing shortage, we began production of VTM in-house in support of diagnostic testing in our hospital network. As our diagnostic laboratory was not equipped for reagent production, we took advantage of space and personnel that became available due to closure of the research division of our medical center. We utilized a formulation of VTM described by the CDC that was simple to produce, did not require filtration for sterilization, and used reagents that were available from commercial suppliers. Performance of VTM was evaluated by several quality assurance measures. Based on cycle threshold (CT ) values of spiking experiments, we found that our VTM supported highly consistent amplification of the SARS-CoV-2 target (coefficient of variation = 2.95%) using the Abbott RealTime SARS-CoV-2 Emergency Use Authorization (EUA) assay on the Abbott m2000 platform. VTM was also found to be compatible with multiple swab types and, based on accelerated stability studies, able to maintain functionality for at least 4 months at room temperature. We further discuss how we met logistical challenges associated with large-scale VTM production in a crisis setting, including use of a staged assembly line for VTM transport tube production.

Using quantitative polymerase chain reaction (qPCR) and occupancy models to estimate atypical Aeromonas hydrophila (aAh) prevalence in catfish

A strain of atypical Aeromonas hydrophila (aAh) has caused issues within the channel catfish Ictalurus punctatus industry of the southeastern United States since 2009. These atypical pathotypes cause acute mortality events resulting in catastrophic losses, as opposed to more chronic mortality and lesions seen in typical infections of motile aeromonas septicemia (MAS). This study provides a basic framework for rapid field sampling negating the need for re-isolation or enrichment culture, thereby reducing the time between sampling and detection. Rapid and accurate quantitative PCR based methods for detection of aAh have been described and are important confirmative tools in research and diagnostic settings. These methods also have application in epidemiological surveys investigating the spread of disease and elucidating pathogen dynamics that may lead to outbreaks. To date, no field-based sampling technique for rapid aAh detection in resident pond populations has been explored. In this study, culture swabs taken from the gills and lower intestine of pond-raised catfish were assessed for their suitability as rapid field-based collection methods for downstream applications. Results showed the state of the pond has a significant effect on which swab location yields the highest proportion of PCR positive results. During an active outbreak, gill swabs identified more fish as aAh-positive; however, in apparently healthy populations, swabs taken from the lower intestine identified significantly more aAh-positive fish than gill swabs, despite no statistical difference in the concentration of aAh cell equivalents between swab sites. Naïve prevalence estimates from the two swab types were compared to estimates provided by a hierarchical occupancy model. Prevalence estimates from gill swabs was 0.95% while vent swabs showed a prevalence of 2.2%; however, estimates based on the occupancy model were 6.6% and 9.8%, respectively. This multi-fold increase in prevalence estimates highlights the importance of accounting for imperfect detection in epidemiological studies and in assessing potential outbreak risk. Furthermore, occupancy models based on these data indicate resident fish can be aAh-positive carriers with no gross signs of infection, providing evidence aAh can reside in catfish ponds in the absence of disease. The presence of a carrier state indicates the pathogen may pose minimal risk to the host is compromised or a mechanical portal of entry into the blood stream is available. This provides an important direction for future research in understanding the mechanisms of aAh outbreaks in catfish aquaculture ponds.

Rapid Large-Scale COVID-19 Testing During Shortages.

The Coronavirus disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has resulted in economic and social lockdowns in most countries all over the globe. Early identification of infected individuals is regarded as one of the most important prerequisites for fighting the pandemic and for returning to a ‘New Normal’. Large-scale testing is therefore crucial, but is facing several challenges including shortage of sample collection tools and of molecular biological reagents, and the need for safe electronic communication of medical reports. We present the successful establishment of a holistic SARS-CoV-2 testing platform that covers proband registration, sample collection and shipment, sample testing, and report issuing. The RT-PCR-based virus detection, being central to the platform, was extensively validated: sensitivity and specificity were defined as 96.8% and 100%, respectively; intra-run and inter-run precision were <3%. A novel type of sample swab and an in-house-developed RNA extraction system were shown to perform as good as commercially available products. The resulting flexibility guarantees independence from the current bottlenecks in SARS-CoV-2 testing. Based on our technology, we offered testing at local, national, and global levels. In the present study, we report the results from approx. 18,000 SARS-CoV-2 tests in almost 10,000 individuals from a low-frequency SARS-CoV-2 pandemic area in a homogenous geographical region in north-eastern Germany for a period of 10 weeks (21 March to 31 May 2020). Among the probands, five SARS-CoV-2 positive cases were identified. Comparative analysis of corresponding virus genomes revealed a diverse origin from three of the five currently recognized SARS-CoV-2 phylogenetic clades. Our study exemplifies how preventive SARS-CoV-2 testing can be set up in a rapid and flexible manner. The application of our test has enabled a safe maintenance/resume of critical local infrastructure, e.g., nursing homes where more than 5000 elderlies and caretakers got tested. The strategy outlined by the present study may serve as a blueprint for the implementation of large-scale preventive SARS-CoV-2 testing elsewhere.

Factors affecting DNA recovery from cartridge cases

Cartridge cases are often the sole items left behind after a shooting incident and DNA traces from these can identify persons connected to the shooting. However, the chance of retrieving usable DNA profiles from cartridge cases is limited, due to the low amounts of deposited DNA and subsequent DNA loss associated with the firing process. In the current study, we set out to increase the DNA recovery from cartridge cases and cartridges by evaluating different swab types and detergents used for trace collection. A protocol applying nylon-flocked swabs instead of cotton swabs was implemented in casework at the Swedish National Forensic Centre (NFC), increasing DNA yield. The number of samples providing a DNA concentration ≥ 0.001 ng/μL (the in-house cut-off for processing low-template samples) increased from 11.1 to 28.6 % for cartridge cases and from 16.0 to 43.3 % for cartridges. There was also a substantial increase in mixed STR profiles, too complex to use for comparisons. Thus, it was not possible to take the full advantage of the elevated DNA yield provided by nylon-flocked swabs. The number of usable STR profiles increased from 5.0 to 8.0 % for cartridge cases and remained unchanged for cartridges. Controlled studies were performed to assess the impact on the DNA recovery from different persons handling the ammunition, different material and size of the cartridge cases, and the type of firearm used. These studies reflected an ideal situation, where all cartridges were extensively handled and loaded without gloves, thus providing a higher expected DNA yield compared to most casework samples. The total peak height differed by up to a factor of ∼50 when 20 different persons handled cartridges prior to shooting. By evaluating eleven combinations of different firearms and ammunition, it was found that the casing material and type of firearm also have a substantial impact on DNA yield.

Pooling of Laying Hen Environmental Swabs and Efficacy of Salmonella Detection

Environmental testing for Salmonella Enteritidis is required for U.S. shell egg producers with ≥3,000 hens on a farm. The egg producer assumes all costs for the mandatory testing. According to the U.S. Food and Drug Administration (FDA) Egg Rule, either manure scraper or drag swabs can be collected according to published guidelines and requirements. The present study was undertaken to determine the efficacy of Salmonella detection with one-, two-, and four-swab pools of either manure scraper or drag swabs. Resistant isolates of Salmonella serovars Enteritidis (1,000 ppm of streptomycin), Heidelberg (200 ppm of nalidixic acid [NA]), Typhimurium (200 ppm of NA), and Kentucky (200 ppm of NA) were utilized. Low (approximately 8.4 CFU) and high (approximately 84 CFU) levels of inocula were introduced onto a single swab within a pool. Single flocks from each conventional cage (manure scraper swabs) and cage-free barn (drag swabs) were monitored throughout the study at the ages required under the FDA Egg Rule. The highest and most consistent recovery of inoculum was found in single swab samples. For low dose inocula, recovery of isolates was low from single manure scraper swabs (57.9 to 29.2%) and decreased as more swabs were added to the pool. Recovery of isolates from manure scraper swabs was higher for high dose inocula, although Salmonella Heidelberg was outcompeted by the naturally occurring flora and had the lowest rate of recovery among the isolates tested. One- and two-swab pools of drag swabs had similar rates of recovery at both low and high doses for Salmonella Enteritidis, Salmonella Heidelberg, and Salmonella Typhimurium. When Salmonella Enteritidis and Salmonella Kentucky were combined in an inoculum, Salmonella Enteritidis was recovered at a much higher rate than was Salmonella Kentucky for all types of swabs and doses of inocula. Pooling of two drag swabs allowed for similar detection of low and high dose Salmonella, but the pooling of manure scraper swabs decreased detection of low dose Salmonella.

The influence of a swab type on the results of point-of-care tests

Most point-of-care tests (POCT) use swabs for sampling and/or for applying a sample on the test. A variety of swabs differing in tip materials is commercially available. Different tip materials have different chemical and physical characteristics which might influence the specimen collection and release. We investigated properties of various types of swabs used in clinical diagnostics with focusing on two kinds of analytes, DNA and proteins, which are most often used targets in POCT. As the model samples we used diphtheria toxoid NIBSC 69/017 for investigating recovery of protein analytes such as antigens and bacterial strains of Escherichia coli ATCC 25922, diphtheria toxin-producing Corynebacterium diphtheriae NCTC 10648, and the clinical isolate nontoxigenic C. diphtheriae 5820/15 for investigating the recovery of nucleic acids. We investigated four types of swabs most commonly used in clinical diagnostics in terms of absorption capacity and efficiency of release of nucleic acids and proteins. Volume uptake was measured in milligrams. For DNA release various washing out buffers were used and the amount of released DNA was measured spectrophotometrically. The amount of protein released from the swabs were examined using the Lowry assay. We observed statistically significant differences (p < 0.05) in the mean weights of absorbed liquid, in the DNA recovery and protein recovery by the four variety of swab examined. However, the efficiency of DNA and protein release was not correlated to the absorbed volume of a sample, but rather to the properties of swabs. The swab composition and structure can have a significant impact on the collection and release efficiency of a sample. Therefore, validation of POCT in relation to the used swabs for sampling is really important. The use of inappropriate swabs could lead to false negative or misleading analysis results.

An improved process for the collection and DNA analysis of fired cartridge cases

Improvements to the DNA analysis of fired cartridge cases have been made in recent years, yet successful analysis of this important evidence type remains difficult. In this study, we describe both a novel device for the collection and transport of fired cartridge cases and a new DNA recovery method that incorporates a rinse-and-swab technique. This technique combines two different types of swabs and a rinse solution with additives that reduce the degradative effects that copper has on DNA. The new recovery method yielded approximately threefold more DNA than the traditional double swab method and reduced the evidence of degradation. After validation, we estimated the real-world success rate of obtaining DNA profiles suitable for comparison with the rinse-and-swab method by testing over 100 cartridge cases collected from crime scenes. Approximately 67 % of the time (8 of 12), at least one DNA profile suitable for comparison was obtained from fired cartridge cases assumed to be associated with a single firearm using the collection device and the rinse-and-swab method when the fired cartridge cases were collected within 24 h.

Efficacy of "touch" DNA recovery and room-temperature storage from assault rifle magazines.

Crimes committed with assault rifles are becoming increasingly prevalent in the United States. In the absence of other evidence, DNA analysis can often provide informative leads. Unfortunately, any DNA transferred to rifle components left behind at a crime scene is likely to be low in quantity and/or quality. Furthermore, collected evidence is unlikely to be processed immediately and may require storage. Long-term storage can subject DNA to damage and degradation, which ultimately affects DNA profile interpretation and may prevent the identification of potential suspects. This study assessed the ability of a new swab storage device, the SwabSaver®, to preserve "touch" DNA from AR-15 magazine rifles using three different collection devices. Three volunteers loaded bullet cartridges into plastic polymer and aluminum AR-15 magazines. DNA was collected with traditional cotton swabs, layered cotton paper swabs, or nylon-flocked swabs. Collection devices were then stored at room-temperature for up to two months in either the SwabSaver® device or an empty centrifuge tube. The results suggest that substrate and swab type had less of an effect on profile completeness than storage type. Furthermore, SwabSaver® storage yielded DNA quantities comparable to "touch" DNA extracted after 24h.

Avian Influenza Virus Sample Types, Collection, and Handling.

Successful detection of avian influenza (AI) virus, viral antigen, nucleic acid, or antibody is dependent upon the collection of the appropriate sample type, the quality of the sample, and the proper storage and handling of the sample. The diagnostic tests to be performed should be considered prior to sample collection. Sera are acceptable samples for ELISA or agar gel immunodiffusion tests, but not for real-time RT-PCR. Likewise, swabs and/or tissues are acceptable for real-time RT-PCR and virus isolation. The sample type will also depend on the type of birds that are being tested; oropharyngeal swabs from gallinaceous poultry and cloacal swabs from waterfowl are the preferred specimens for most diagnostic tests, although it is optimal to collect swabs from both locations, if possible. In addition to collecting the appropriate sample for the tests to be performed, selecting the right materials for sample collection (i.e., type of swab) is very important. This chapter will outline the collection of different specimen types and procedures for proper specimen handling.

Evaluation of Swab and Rinse Sampling Procedures and Recovery Rate Determination in Cleaning Validation Considering Various Surfaces, Amount and Nature of the Residues and Contaminants.

A cleaning validation for a family of compounds utilizing swab sampling and rinse solution procedures, and high performance liquid chromatography for separation and detection of the analytes was performed.Effective parameters on recovery including sampling method, swab characteristics, solvent, swabbing technique, and material substance of product contact surfaces within the manufacturing equipment for swab and rinse sampling method, quantitative cleaning verification method, and active pharmaceutical ingredient (API) level and nature have been studied.The limit of detection and the limit of quantitation for the HPLC method were determined to be 0.0198 µg/mL, and 0.0495 µg/mL of the analyte, respectively. The linearity on replicate injections of the standard prepared in the range of 0.78, 1.55, 3.1, and 6.2 µg/mL, and relative standard deviation (R.S.D.) found to be 1.2, 1.0, 0.9, and 0.6, respectively with correlation coefficient of R2 = 0.9999. Recovery coverage for each type of surface was acceptable, ranging from 63.88% for swab sampling of stainless steel to 97.85% for rinse sampling of PVC. The acceptance criteria for precision on replicate injections of the analyte prepared in three concentration levels covering the specified range of 50, 100, and 200% was successfully accomplished R.S.D. lower than 15% for recovery results.Thus, choosing the appropriate sampling method, swab type, and surface condition can affect and increase recovery rate determination efficiency.