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

Evaluation of metal ions and DNA recovery from the surface of fired and unfired brass ammunition to improve STR profiling

Interest in recovering DNA from the surface of ammunition evidence for genotyping has increased over the past few years. Numerous studies have examined a variety of methods to maximize DNA recovery from these types of challenging samples, but successful DNA profiling has been inconsistent. Low amounts of DNA and PCR inhibition due to metal ions have been suggested as the leading causes of poor results; however, no study quantitatively examined the presence of metal ions at various stages of the DNA analysis workflow from DNA collection through to amplification. In this study, the effectiveness of six different DNA collection and purification methods commonly used by forensic laboratories to process brass ammunition for DNA evidence was investigated. The amount of copper, zinc, and other metals co-recovered from fired and unfired brass casings during DNA collection (using numerous soaking, swabbing, and direct PCR protocols) was quantified via Inductively Coupled Plasma - Optical Emission Spectrometry (ICP-OES). This same panel of metals was subsequently quantified after DNA lysis and purification steps. Results demonstrated that low amounts of DNA, DNA damage, and degradation are more detrimental to STR typing results than PCR inhibition, as metal ions were successfully removed by all DNA purification methods tested. Furthermore, the use of metal ion chelators increased the amount of DNA recovered and number of reportable STR alleles. This research informs the forensic community on the most effective way to collect and process trace amounts of biological material from brass ammunition and similar evidence.

The impact of substrate characteristics on the collection and persistence of biological materials, and their implications for forensic casework

This study assessed the level of nucleic acid persistence on the substrate pre-, and post-swabbing, in order to assess whether biological materials (touch, saliva, semen, and blood) are collected differently depending on the substrate characteristics. A total of 48 samples per deposit and substrate variety (n = 384) were assessed by tracking the persistence of nucleic acid using Diamond™ Nucleic Acid Dye (DD) staining and Polilight photography. The number of DD nucleic acid fluorescent complexes formed post-staining were counted (fluorescent count) and in conjunction with the fluorescence signal intensity (DD nucleic acid complex accumulation) used to estimate the level of nucleic acid persistence on substrates. Touch deposits have shown to be the most persistent deposit with strong adhesion capabilities on both substrate verities. Saliva displayed a higher persistence than semen and/or blood. Semen displayed a high collection efficiency as well as a high fluorescence signal intensity. Blood displayed a low persistence on both substrates with a superior collection efficiency that may also indicate a higher probability to become dislodged from surfaces given a particular activity. Our research has shown that the persistence and recovery of biological deposits is not only measurable but more importantly, may have the potential to be estimated, as such, may build an understanding that can provide valuable guidance for collection efficiency evaluations, and the assessing of the probability of particular profiles, given alternate propositions of means of transfer occurring.

Salmon sperm DNA increases sample recovery from cotton swabs

Forensic samples with low DNA template amounts are difficult to analyze and interpret. There is a large body of research demonstrating that adding carrier nucleic acid to storage tubes, solid phase extractions, or filtering devices can improve yields of target DNA. However, the addition of carrier nucleic acid to sampling substrates, like cotton swabs, has not yet been attempted. In this proof-of-concept study, carrier nucleic acids in the form of either Poly (A) RNA or salmon sperm DNA were spotted onto cotton swabs, followed by human genomic DNA, to determine if introducing the carrier prior to sample collection would increase recovery from the swabs post-extraction. Extracts were also evaluated to determine whether adding the carrier nucleic acids to human DNA would interfere with downstream forensic DNA analysis processes such as real-time PCR quantitation, PCR amplification of STR loci, or capillary electrophoresis. The RNA carrier did not improve human sample recovery from cotton swabs. The extraction efficiency of human DNA from cotton swabs was increased when the DNA carrier was applied to the swabs prior to sample deposition, and the scale of the increase depended on the amount of carrier DNA used. When applying the salmon sperm DNA carrier to cotton swabs, with each increase from no carrier to 0.001-1-10 µg, human DNA recovery went from ∼29 % to ∼50 % to ∼75 % to ∼100 %. Additionally, no inhibitory effects from the carrier DNA were observed post-extraction with quantitation or in the DNA profile after amplification. Therefore, salmon sperm DNA carrier will increase human DNA yield from cotton swabs without negative effects on downstream forensic DNA profiling methods, with the optimal carrier amount being 10 µg.

Safety tests and clinical research on buccal and nasal microneedle swabs for genomic analysis

Conventional swabs have been used as a non-invasive method to obtain samples for DNA analysis from the buccal and the nasal mucosa. However, swabs may not always collect pure enough genetic material. In this study, buccal and nasal microneedle swab is developed to improve the accuracy and reliability of genomic analysis. A cytotoxicity test, a skin sensitivity test, and a skin irritation test are conducted with microneedle swabs. Polymer microneedle swabs meet the safety requirements for clinical research and commercial use. When buccal and nasal microneedle swabs are used, the amount of genetic material obtained is greater than that from commercially available swabs, and DNA purity is also high. The comparatively short microneedle swab (250 μm long) cause almost no pain to all 25 participants. All participants also report that the microneedle swabs are very easy to use. When genotypes are compared at five SNP loci from blood of a participant and from that person's buccal or nasal microneedle swab, the buccal and nasal microneedle swabs show 100% concordance for all five SNP genotypes. Microneedle swabs can be effectively used for genomic analysis and prevention through genomic analysis, so the utilization of microneedle swabs is expected to be high.

A holistic approach for the selection of forensic DNA swabs

In the present study, we compared the performance of five different ISO 18385 certified forensic swabs for DNA sampling in practice over a time period of five months. Comparisons were made for DNA profiling success rates, measured as the percentage of CODIS (Combined DNA Index System) suitable profiles as well as for practical suitability during sampling at the scene, measured through a survey among collaborators. More than forty members of our crime scene investigation (CSI) unit took part in the test series and provided structured feedback concerning different aspects of swab handling. A total number of 1094 "touch" DNA samples have been subjected to DNA analysis. Swabs performed significantly different in terms of DNA profiling success rates. We also observed significant differences in DNA extraction efficiency between swabs. The evaluation by the collaborators of various aspects of handling differed significantly between swabs. We can assume that a more convenient handling decreases the risk of contamination or sample mislabelling and increases sampling efficiency and staff satisfaction. Our results demonstrate that the selection of disposable sampling devices such as forensic swabs for DNA sampling should be made based on a holistic approach. To be able to select the best performing swab for a given combination of CSI and DNA laboratory procedures, it might not be sufficient to only perform DNA extraction comparisons and trace sampling under controlled laboratory conditions.

Improvements, factors, and influences on DNA recovery from firearms

Touch DNA recovery from firearms can be central to many criminal investigations, yet the generation of DNA profiles from these items remains poor. Currently in Australia, published casework data highlights extremely poor DNA success from samples recovered from firearms. Only between 5% and 25% of samples result in useful DNA data and therefore increasing the success of DNA recovered from firearms is highly important but has not yet been explored in-depth. This study focused on increasing the recovery of DNA from ten firearm components that were held for 15 s. Multiple recovery methods were used, and the resulting genetic data compared. DNA evidence may be deliberately removed from firearms after discharge to hamper forensic investigations, therefore this study examined the effect of wiping down the components or handling them with gloves. A standard double swab and rinse swab recovery method resulted in an average of 73% cellular recovery. A cumulative swab process had the highest average recovery at 86%, although it was found that increasing the DNA yield led to an increase in mixture complexity. Wiping over the components was observed to remove on average 69% of cellular material, compared with 33% when handed with gloves. However, the size and texture of the components affected the efficiency of cellular material removal. The results from this study allow for prioritisation of areas to sample on firearms, as well as suggesting techniques that can be applied for the optimum process of cellular recovery and subsequent generation of STR DNA data.

Towards an affinity-free, centrifugal microfluidic system for rapid, automated forensic differential extraction

Biological evidence originating from victims of sexual assault is often comprised of unbalanced cellular mixtures with significantly higher contributions from the victim's genetic material. Enrichment of the forensically-critical sperm fraction (SF) with single-source male DNA relies on differential extraction (DE), a manually-intensive process that is prone to contamination. Due to DNA losses from sequential washing steps, some existing DE methods often fail to generate sufficient sperm cell DNA recovery for perpetrator(s) identification. Here, we propose an enzymatic, 'swab-in' rotationally-driven microfluidic device to achieve complete, self-contained, on-disc automation of the forensic DE workflow. This 'swab-in' approach retains the sample within the microdevice, enabling lysis of sperm cells directly from the evidence cutting to improve sperm cell DNA yield. We demonstrate clear proof-of-concept of a centrifugal platform that provides for timed reagent release, temperature control for sequential enzymatic reactions, and enclosed fluidic fractionation that allows for objective evaluation of the DE process chain with a total processing time of ≤15 min. On-disc extraction of buccal or sperm swabs establishes compatibility of the prototype disc with: 1) an entirely enzymatic extraction method, and 2) distinct downstream analysis modalities, such as the PicoGreen® DNA assay for nucleic acid detection and the polymerase chain reaction (PCR).

Development of Improved DNA Collection and Extraction Methods for Handled Documents

Handwritten documents may contain probative DNA, but most crime laboratories do not process this evidence. DNA recovery should not impair other evidence processing such as latent prints or indented writing. In this study, single fingermarks on paper were sampled with flocked swabs, cutting, and dry vacuuming. In addition, two extraction methods were compared for the sample type. DNA yields were low across all methods; however, this work confirms the ability to recover DNA from paper and the usefulness of the vacuum sampling method combined with the Chelex-Tween method. Stability of touch DNA deposits were compared over an 11-month period to better understand degradation that may occur over time. No significant difference in DNA recovery was observed, suggesting DNA deposits on paper are stable over an 11-month span.

Tracing the origin of large respiratory droplets by their deposition characteristics inside the respiratory tract during speech

Origin of differently sized respiratory droplets is fundamental for clarifying their viral loads and the sequential transmission mechanism of SARS-CoV-2 in indoor environments. Transient talking activities characterized by low (0.2 L/s), medium (0.9 L/s), and high (1.6 L/s) airflow rates of monosyllabic and successive syllabic vocalizations were investigated by computational fluid dynamics (CFD) simulations based on a real human airway model. SST k-ω model was chosen to predict the airflow field, and the discrete phase model (DPM) was used to calculate the trajectories of droplets within the respiratory tract. The results showed that flow field in the respiratory tract during speech is characterized by a significant laryngeal jet, and bronchi, larynx, and pharynx-larynx junction were main deposition sites for droplets released from the lower respiratory tract or around the vocal cords, and among which, over 90% of droplets over 5 µm released from vocal cords deposited at the larynx and pharynx-larynx junction. Generally, droplets' deposition fraction increased with their size, and the maximum size of droplets that were able to escape into external environment decreased with the airflow rate. This threshold size for droplets released from the vocal folds was 10-20 µm, while that for droplets released from the bronchi was 5-20 µm under various airflow rates. Besides, successive syllables pronounced at low airflow rates promoted the escape of small droplets, but do not significantly affect the droplet threshold diameter. This study indicates that droplets larger than 20 µm may entirely originate from the oral cavity, where viral loads are lower; it provides a reference for evaluating the relative importance of large-droplet spray and airborne transmission route of COVID-19 and other respiratory infections.

A thread-based electrofluidic platform for direct transfer, separation, and pre-concentration of materials from sample swabs

A new method and platform has been developed for direct transfer, electrophoretic separation, and pre-concentration of swabbed samples using the principles of thread-based electrofluidics. A direct electrokinetic injection has been observed for a variety of analytes ranging from small molecules to proteins. The effect of physicochemical interactions of the analyte with the swab and the thread on the transfer efficiency has been studied by exploring different swab and thread combinations. For fluorescein, using a polyurethane swab, 98% and 94% transfer efficiencies were observed on mercerised cotton and nylon thread, while only 80% transfer efficiency was observed on polyester thread, respectively. A 97% transfer of fluorescein was observed on the nylon thread when a flocked nylon swab was used, while only 47% transfer was observed when a cotton swab was used. A successful transfer has been observed for both liquid and dry samples from either pre-wetted or dry swabs in both the presence and absence of any surrounding electrolytes. The platform has been further adapted for multiplexed analysis, where a sample from a single swab was transferred onto two parallel thread systems with ca. 50% distribution between them. The method has been validated for transfer, separation, and pre-concentration of DNA from blood. It has also been successfully used to directly analyse dried blood samples using a commercial sampling device, Neoteryx Mitra.

An improved rapid method for DNA recovery from cotton swabs

We present a novel rapid method for the recovery of cellular and free DNA from cotton swabs based on a simple elution buffer containing a high molecular weight polymer and detergent combined with a short proteinase K digestion to release cellular DNA. This method shows increased yields approaching 80% recovery of the input DNA compared to the QIAamp DNA Mini kit standard extraction protocol for swabs which has a recovery of 20-30%. The buffer components in the described method are compatible with direct PCR analysis of the isolated DNA without further purification. Recovery efficiencies were estimated by qPCR.

Pulse Lavage System (PLS) versus forensic wet-vacuum collection of biological material

Wet-vacuum collection of forensic biological material has been shown to recover greater total DNA yields compared to traditional methods, such as wet swabbing. The Pulse Lavage System (PLS), an orthopedic surgical instrument, was evaluated in comparison to a forensic wet-vacuum device for the DNA collection and recovery of diluted bloodstains from seven substrates of varying porosity. Three different PLS models were evaluated, and each model yielded DNA concentrations which were comparable to the forensic wet-vacuum system, recovering 79-99 % relative to the wet-vacuum, which were overall not statistically different. Our results suggest that the PLS, though intended for medical use, has the potential to serve as an affordable alternative to the forensic wet-vacuum system. However, additional evaluation and modification to the PLS collection method may be warranted for complete optimization.

The DNA-Buster: The evaluation of an alternative DNA recovery approach

Touch DNA recovery techniques can have limitations, as their effectiveness depends on the substrate on which the DNA of a person of interest can be found. In this study, an in-house dry-vacuuming device, the DNA-Buster, was compared to traditional methods for its DNA recovery performance from items typically examined in forensic casework. The aim was to evaluate whether this dry-vacuuming approach can recover DNA efficiently, potentially complementing the well-established recovery strategies. For this, the performances of swabbing, taping, wet- (M-Vac®) and dry-vacuuming (DNA-Buster) were investigated quantitatively and qualitatively for touch DNA deposited on carpet, cotton sweater, stone, tile and wood. For the sweater, both vacuuming methods outperformed the other collection tools quantitatively. While the highest DNA amounts for the carpet were yielded by swabbing and taping, dry-vacuuming was equally good in reaching full DNA profiles, whereas less complete profiles were observed for the M-Vac®. For stone and tile, swabbing was optimal, whereas dry-vacuuming clearly underperformed for these substrates. Taping was the best recovery method for wood. Despite applying single donor DNA after thoroughly cleaning the items, undesired DNA mixtures were detected for all recovery techniques and all substrates. The overall research findings show first that the novel dry-vacuuming method is suited for DNA recovery from textiles. Secondly, they indicate that more attention should be paid to the substrate-collection dependency to ensure best practices in recovering genetic material in a precise, confident and targeted manner from the variety of forensic casework material.

Portable capillary electrophoresis coupled with swab-based extraction device for cleaning validation in pharmaceutical facilities

All pharmaceutical manufacturers are required to verify that their production equipment is free from contaminants. Here, we report the capability of a fully automated portable capillary electrophoresis instrument with an integrated sample swab extraction - the Grey Scan ETD-100 - for the detection of pharmaceutical residues on surfaces of manufacturing equipment. Lidocaine was used as a model compound and could be recovered from a surface by swabbing, extracted from the swab, and analysed within 1 min. The recovery of lidocaine from a stainless-steel coupon was 81.3 %, with a LOD of 0.13 µg/swab. This fast, sensitive, and simple method implemented on a user-friendly portable CE instrument without the need for manual sample pre-treatment provides the possibility for on-site rapid determination of equipment cleanliness in the pharmaceutical industry.

Application of vaginal tampon as an alternative to nasal swabs for higher recovery of DNA from sheep and goats for PCR based diagnosis of bovine tuberculosis

A study was conducted to find the applicability of vaginal tampons as an alternative to regular cotton swabs as a nasal secretion collection tool for the higher recovery of DNA. Nasal secretions were collected from sheep and goats using regular cotton swab and tampon swab. The mean yield and purity of the DNA extracted from tampon were significantly higher than that of the DNA extracted from cotton swab. The tampon swabs resulted higher DNA recovery than the cotton swabs after they were allowed to absorb M. bovis culture. The tampon swab was also found to be more sensitive in detecting M. bovis by PCR. This study concluded that vaginal tampons are having a higher absorption capacity with more DNA yield and can be used as a nasal swab in the diagnosis of bovine tuberculosis.

Optimization of DNA extraction and sampling methods for successful forensic microbiome analyses of the skin and saliva

Microbiome studies have contributed to many fields, such as healthcare and medicine; however, these studies are relatively limited in forensics. Microbiome analyses can provide information, such as geolocation and ancestry information, when short tandem repeat (STR) profiling fails. In this study, methods for DNA extraction and sampling from the skin and saliva were optimized for the construction of a Korean Forensic Microbiome Database (KFMD). DNA yields were estimated using four DNA extraction kits, including two automated kits (Maxwell® FSC DNA IQ™ Casework Kit and PrepFiler™ Forensic DNA Extraction Kit, updated) and two manual kits (QIAamp DNA Mini Kit and QIAamp DNA Micro Kit) commonly used in forensic DNA profiling laboratories. Next-generation sequencing of the 16S rRNA V4 region was performed to analyze microbial communities in samples. The Bacterial Transport Swab with Liquid Media (NobleBio), two cotton swabs (PoongSung and Puritan), and nylon-flocked swabs (NobleBio and COPAN) were tested for DNA recovery. The PrepFiler and Maxwell kits showed the highest yields of 3.884 ng/μL and 23.767 ng/μL from the scalp and saliva, respectively. With respect to DNA recovery, nylon-flocked swabs performed better than cotton swabs. The relative abundances of taxa sorted by DNA extraction kits were similar contributions; however, with significant differences in community composition between scalp and saliva samples. Lawsonella and Veillonella were the most abundant genera in the two sample types. Thus, the Maxwell® FSC DNA IQ™ Casework Kit and nylon-flocked swab (NobleBio) were optimal for DNA extraction and collection in microbiome analyses.

Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review

The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.

Comparison of the certified Copan eSwab system with commercially available cotton swabs for the detection of multidrug-resistant bacteria in rectal swabs

BACKGROUND

Rectal swabs are well-implemented screening tools for multidrug-resistant bacteria (MDRB). Since certified swabs such as the Copan eSwab system experienced a delivery bottleneck during the COVID-19 pandemic, commercially available alternatives such as commonly used double-tipped cotton swabs had to be investigated, especially considering their similarity to professional cotton swabs for microbiological purposes.

METHODS

Diagnostic properties of commercial cotton swabs (comparable to Q-tips) and Copan eSwabs were qualitatively compared in a prospective single-center study using microbiological standard cultures and PCR methods for the detection of multidrug-resistant Gram-negative bacteria and vancomycin-resistant enterococci (VRE).

RESULTS

A total of 196 swab pairs were collected from 164 participants. MDRB were detected in 36 of 164 cases (22%). There were neither false-negative nor false-positive results using commercial cotton swabs. In 8 of 196 samples (4.1%) MDRB species were detected only by using cotton swabs, including vancomycin-resistant Enterococcus faecium, OXA-48 producing Escherichia coli, ESBL-producing Klebsiella pneumoniae and ESBL-producing Escherichia coli.

DISCUSSION

Commercial cotton swabs turned out to be a reliable alternative to Copan eSwabs. For practical use as a screening tool, relevant storage- and manufacturer-related contamination must be ruled out beforehand.

CONCLUSIONS

Commonly available double-tipped cotton swabs can be used for rectal MDRB screening in the event of supply shortages of certified swabs. Further studies should clarify their suitability as a sampling system for nasopharyngeal MRSA carriage or even for the molecular biological detection of SARS-CoV-2.

Environmental Persistence of Monkeypox Virus on Surfaces in Household of Person with Travel-Associated Infection, Dallas, Texas, USA, 2021

In July 2021, we conducted environmental sampling at the residence of a person in Dallas, Texas, USA, who had travel-associated human West African monkeypox virus (MPXV-WA). Targeted environmental swab sampling was conducted 15 days after the person who had monkeypox left the household. Results indicate extensive MPXV-WA DNA contamination, and viable virus from 7 samples was successfully isolated in cell culture. There was no statistical difference (p = 0.94) between MPXV-WA PCR positivity of porous (9/10, 90%) vs. nonporous (19/21, 90.5%) surfaces, but there was a significant difference (p<0.01) between viable virus detected in cultures of porous (6/10, 60%) vs. nonporous (1/21, 5%) surfaces. These findings indicate that porous surfaces (e.g., bedding, clothing) may pose more of a MPXV exposure risk than nonporous surfaces (e.g., metal, plastic). Viable MPXV was detected on household surfaces after at least 15 days. However, low titers (<10² PFU) indicate a limited potential for indirect transmission.

Comparison of swab types & elution buffers for collection and analysis of intact cells to aid in deconvolution of complex DNA mixtures

Heightened sensitivity of forensic DNA techniques has led to an increased variety of samples tested, often yielding complex DNA mixtures, in turn making the interpretation of profiling results more complicated. Currently, there is no prescribed upstream laboratory method to separate complex DNA mixtures by their contributors; therefore, a method is needed that could reduce mixtures into their component parts. Various cell sorting applications have the potential to be this method, if intact cells can be reliably obtained from forensic samples. Here, the effects of elution buffer and swab substrate on the recovery of intact, human, white blood cells from dried blood samples were evaluated. Approximately 328,000 cells per swab were deposited onto cotton, flocked, and dissolvable swabs. The whole-cell elution of the dried samples was evaluated with water, phosphate buffered saline, and AutoMACS® elution buffers. We demonstrate that AutoMACS® buffer is superior for the elution of intact cells, compared to phosphate buffered saline and water. When swab type was considered, the highest yield of intact cells resulted from flocked swabs, as opposed to cotton or dissolvable swabs.

Evaluation of the Effects of Different Sample Collection Strategies on DNA/RNA Co-Analysis of Forensic Stains

The aim of this study was to evaluate the impact of different moistening agents (RNase-free water, absolute anhydrous ethanol, RNAlater^®) applied to collection swabs on DNA/RNA retrieval and integrity for capillary electrophoresis applications (STR typing, cell type identification by mRNA profiling). Analyses were conducted on whole blood, luminol-treated diluted blood, saliva, semen, and mock skin stains. The effects of swab storage temperature and the time interval between sample collection and DNA/RNA extraction were also investigated. Water provided significantly higher DNA yields than ethanol in whole blood and semen samples, while ethanol and RNAlater^® significantly outperformed water in skin samples, with full STR profiles obtained from over 98% of the skin samples collected with either ethanol or RNAlater^®, compared to 71% of those collected with water. A significant difference in mRNA profiling success rates was observed in whole blood samples between swabs treated with either ethanol or RNAlater^® (100%) and water (37.5%). Longer swab storage times before processing significantly affected mRNA profiling in saliva stains, with the success rate decreasing from 91.7% after 1 day of storage to 25% after 7 days. These results may contribute to the future development of optimal procedures for the collection of different types of biological traces.

The effect of NucleoSpin® Forensic Filters on DNA recovery from trace DNA swabs

Forensic DNA profiling is a globally accepted method for human identification, however, obtaining full DNA profiles from trace DNA can be challenging. The optimal recovery of DNA from trace DNA swabs is therefore crucial. Methods for extracting DNA from swabs often make use of a spin basket combined with a centrifugation step, to enhance the release of cells from the swab prior to DNA extraction. The NucleoSpin® Forensic Filter (Macherey-Nagel, Düren) is a type of spin basket, but it has not been thoroughly assessed on trace DNA samples. This study aimed to assess if the inclusion of the NucleoSpin® Forensic Filter significantly improved DNA recovery and DNA profiling success from cotton and flocked swabs used to collect trace DNA and buccal cells (control). Buccal cells and trace DNA samples were collected from 25 volunteers using each swab type (cotton and flocked) in duplicate. DNA was extracted from the samples using the NucleoSpin® DNA Forensic kit, one set with, and the other set without, NucleoSpin® Forensic Filters. DNA concentration was assessed using real time PCR, and DNA profiling was done using the PowerPlex® ESX 16 system. The inclusion of the NucleoSpin® Forensic Filters significantly improved DNA concentration for buccal cells that were collected using flocked swabs (p = 0.035). However, no significant differences were noted for trace DNA samples for either swab type. There was also no significant difference in DNA profiling success when NucleoSpin® Forensic Filters were used, regardless of swab and sample type. These results may be helpful for laboratories that are considering the NucleoSpin® Forensic Filters in the DNA extraction workflow, particularly for trace DNA samples.

Optimizing sample collection methods for detection of respiratory viruses in poultry housing environments

Viral respiratory diseases, such as avian influenza, Newcastle disease, infectious bronchitis, and infectious laryngotracheitis, have considerable negative economic implications for poultry. Ensuring the virus-free status of a premises by environmental sampling after cleaning and disinfection is essential for lifting a quarantine and/or safely restocking the premises following an outbreak. The objectives of this study were to identify optimal sample collection devices and to determine the locations in poultry housing which are best for poultry respiratory virus sample collection. Chickens exposed to infectious bronchitis virus, which was used as a representative virus for enveloped poultry respiratory viruses, were housed in floor-pens in either a curtain-sided wood framed house or a cement block house. Foam swabs, cellulose sponges, polyester swabs, dry cotton gauze and pre-moistened cotton gauze were evaluated for comparative efficiency in recovering viral RNA. Cotton gauze pre-moistened with the viral transport media had the highest sensitivity among the devices (wood-framed house: 78% positive, geometric mean titer [GMT] of 2.6 log₁₀ 50% egg infectious doses [EID₅₀ ] equivalents/ml; cement-block houses: 55% positive, GMT of 1.7 log₁₀ EID₅₀ equivalents/ml). Targeting virus deposition sites is also crucial for efficient virus elimination procedures and subsequent testing, therefore 10 locations within the houses were compared for virus detection. In both housing types the highest viral RNA loads were recovered from the top of drinker lines within the pen. Places the chickens could contact directly (e.g., feeder rim) or were contacted by caretaker feet (hallway floor) also yielded higher levels of viral RNA more consistently. These results will facilitate the establishment of efficient environmental sampling procedures for respiratory viruses of poultry. This article is protected by copyright. All rights reserved.

Special Features of Polyester-Based Materials for Medical Applications

This article presents current possibilities of using polyester-based materials in hard and soft tissue engineering, wound dressings, surgical implants, vascular reconstructive surgery, ophthalmology, and other medical applications. The review summarizes the recent literature on the key features of processing methods and potential suitable combinations of polyester-based materials with improved physicochemical and biological properties that meet the specific requirements for selected medical fields. The polyester materials used in multiresistant infection prevention, including during the COVID-19 pandemic, as well as aspects covering environmental concerns, current risks and limitations, and potential future directions are also addressed. Depending on the different features of polyester types, as well as their specific medical applications, it can be generally estimated that 25–50% polyesters are used in the medical field, while an increase of at least 20% has been achieved since the COVID-19 pandemic started. The remaining percentage is provided by other types of natural or synthetic polymers; i.e., 25% polyolefins in personal protection equipment (PPE).

Development of a Microneedle Swab for Acquisition of Genomic DNA From Buccal Cells

A swab is a tool for obtaining buccal DNA from buccal mucus for biological analysis. The acquisition of a sufficient amount and high quality of DNA is an important factor in determining the accuracy of a diagnosis. A microneedle swab (MN swab) was developed to obtain more oral mucosal tissues non-invasively. Eight types of MN swabs were prepared with varying combinations of patterns (zigzag or straight), number of MNs, intervals of MNs, and sharpness of tips. When MN swab was applied up to 10 times, the tissue amount and DNA yield increased compared to commercial swabs. A zigzag pattern of microneedles was found to be more efficient than a straight pattern and increasing the number of microneedles in an array increased the DNA yield. The MN swab collected about twice the DNA compared to the commercial swab. In an in vivo test using mini pigs, the lower cycle threshold values of mucosal samples collected with MN swabs compared to samples collected with commercial swabs indicated that a greater amount of DNA was collected for SNP genotyping. A polymer MN swab is easy to manufacture by a single molding process, and it has a greater sampling capacity than existing commercial swabs.

The Use of Flocked Swabs with a Protective Medium Increases the Recovery of Live Brucella spp. and DNA Detection

Brucellosis is a worldwide zoonosis caused by bacteria from the genus Brucella. Once established, it is very hard to eradicate this disease, since it contaminates animals, the environment, and humans, causing problems for veterinary and public health as well as wildlife protection programs. Swabs are used for sampling in bacteriological and/or molecular diagnostics, from seropositive animals with disease symptoms, from genitalia or tissue lesions, as well as from contaminated environments. The aim of this study was to compare main of the commercially used swab types for sampling and diagnostics of Brucella spp. and determine the optimal storage conditions and time frame for testing. To achieve this, we tested bacterial and molecular methods for detection of Brucella abortus, Brucella melitensis, and Brucella suis using nine swab types, all with different tip materials, treated immediately after spiking, after 72 h at +4°C, and after 72 h at −20°C. Flocked swabs showed the highest capacity to preserve bacterial viability and DNA quality, regardless the storage conditions. Flocked swabs immersed in a protective medium provided the best conditions for Brucella survival in all three storage conditions. At the same time, the efficacy of quantitative PCR (qPCR) detection for all swabs, including the positive control, was above 50%, irrespective of the storage conditions, while bacterial survival was significantly lowered when swabs were kept at +4°C or −20°C for 72 h (48.2% and 27.5%, respectively). Compared to the positive control and other types, the flocked swabs maintained higher reproducibility regarding their capacity to preserve live bacteria in all three storage conditions.

IMPORTANCE In order to protect public and veterinary health from highly zoonotic bacteria such as members of the genus Brucella and prevent their dissemination into the environment, direct diagnostics are of utmost importance. However, in addition to the highly specific diagnostic tests, the sampling methods, time necessary for specimens to reach the laboratories, and transport conditions are important factors to consider in order to increase the sensitivity of performed tests, especially bacterial culturing and qPCR. This paper shows how different swab types and storage conditions influence classical bacteriological diagnostics of the most prevalent Brucella species – B. melitensis, B. abortus, and B. suis – but have little impact on molecular methods. The presented results highlight (i) the choice of swab regarding the storage and transport conditions, (ii) the importance of immediate swab treatment upon sampling, and (iii) that molecular methods do not depend on storage conditions, unlike classical bacteriological isolation.

Bacterial keratitis: identifying the areas of clinical uncertainty

Bacterial keratitis is a common corneal infection that is treated with topical antimicrobials. By the time of presentation there may already be severe visual loss from corneal ulceration and opacity, which may persist despite treatment. There are significant differences in the associated risk factors and the bacterial isolates between high income and low- or middle-income countries, so that general management guidelines may not be appropriate. Although the diagnosis of bacterial keratitis may seem intuitive there are multiple uncertainties about the criteria that are used, which impacts the interpretation of investigations and recruitment to clinical studies. Importantly, the concept that bacterial keratitis can only be confirmed by culture ignores the approximately 50% of cases clinically consistent with bacterial keratitis in which investigations are negative. The aetiology of these culture-negative cases is unknown. Currently, the estimation of bacterial susceptibility to antimicrobials is based on data from systemic administration and achievable serum or tissue concentrations, rather than relevant corneal concentrations and biological activity in the cornea. The provision to the clinician of minimum inhibitory concentrations of the antimicrobials for the isolated bacteria would be an important step forward. An increase in the prevalence of antimicrobial resistance is a concern, but the effect this has on disease outcomes is yet unclear. Virulence factors are not routinely assessed although they may affect the pathogenicity of bacteria within species and affect outcomes. New technologies have been developed to detect and kill bacteria, and their application to bacterial keratitis is discussed. In this review we present the multiple areas of clinical uncertainty that hamper research and the clinical management of bacterial keratitis, and we address some of the assumptions and dogma that have become established in the literature.

Understanding and utilizing textile-based electrostatic flocking for biomedical applications

Electrostatic flocking immobilizes electrical charges to the surface of microfibers from a high voltage-connected electrode and utilizes Coulombic forces to propel microfibers toward an adhesive-coated substrate, leaving a forest of aligned fibers. This traditional textile engineering technique has been used to modify surfaces or to create standalone anisotropic structures. Notably, a small body of evidence validating the use of electrostatic flocking for biomedical applications has emerged over the past several years. Noting the growing interest in utilizing electrostatic flocking in biomedical research, we aim to provide an overview of electrostatic flocking, including the principle, setups, and general and biomedical considerations, and propose a variety of biomedical applications. We begin with an introduction to the development and general applications of electrostatic flocking. Additionally, we introduce and review some of the flocking physics and mathematical considerations. We then discuss how to select, synthesize, and tune the main components (flocking fibers, adhesives, substrates) of electrostatic flocking for biomedical applications. After reviewing the considerations necessary for applying flocking toward biomedical research, we introduce a variety of proposed use cases including bone and skin tissue engineering, wound healing and wound management, and specimen swabbing. Finally, we presented the industrial comments followed by conclusions and future directions. We hope this review article inspires a broad audience of biomedical, material, and physics researchers to apply electrostatic flocking technology to solve a variety of biomedical and materials science problems.

Nasopharyngeal Swabs vs. Nasal Aspirates for Respiratory Virus Detection: A Systematic Review

Nasal pathogen detection sensitivities can be as low as 70% despite advances in molecular diagnostics. This may be linked to the choice of sampling method. A diagnostic test accuracy review for sensitivity was undertaken to compare sensitivity of swabbing to the nasopharynx and extracting nasal aspirates, using the PRISMA protocol, Cochrane rapid review methodology, and QUADAS-2 risk of bias tools, with meta-analysis of included studies. Sensitivities were calculated by a consensus standard of positivity by either method as the ‘gold standard.’ Insufficient sampling methodology, cross sectional study designs, and studies pooling samples across anatomical sites were excluded. Of 13 subsequently eligible studies, 8 had ‘high’ risk of bias, and 5 had ‘high’ applicability concerns. There were no statistical differences in overall sensitivities between collection methods for eight different viruses, and this did not differ with use of PCR, immunofluorescence, or culture. In one study alone, Influenza H1N1(2009) favored nasopharyngeal swabs, with aspirates having 93.3% of the sensitivity of swabs (p > 0.001). Similarly equivocal sensitivities were noted in reports detecting bacteria. The chain of sampling, from anatomical site to laboratory results, features different potential foci along which sensitivity may be lost. A fair body of evidence exists that use of a different sampling method will not yield more respiratory pathogens.

Touch DNA recovery from vehicle surfaces using different swabs

Several methods of DNA collection are used in places or objects related to crimes, the most common being the use of swabs. However, it is known that the efficacy of touch DNA recovery can be affected by collection devices and surfaces. The aim of this work was to evaluate the efficiency of three different types of swab in recovering touch DNA collected from different parts of a vehicle. The following swabs were tested: PurFlock^® swab (Puritan, USA), 4N6FLOQSwabs™ (Copan S.p.A., Italy), and cotton swab (Labor Import). The experiments were carried out in the same vehicle, using the gearshift knob, the parking brake lever, and the steering wheel as support for the collection of touch DNA. Swabs showed significant differences in the amount of DNA recovered (Hc = 53.52; p < 0.05) and in the rate of allele amplification (Hc = 24.3; p < 0.05). The results indicated a greater DNA recovery efficiency by PurFlock^® swab, followed by cotton, and then 4N6FLOQSwabs™. However, there was no significant difference among the surfaces analyzed. PurFlock^® swab was more efficient for recovering donor alleles than the others (cotton and 4N6FLOQSwabs™), especially for small DNA amounts. This swab was, therefore, suitable for collections in vehicles involved in crime. Furthermore, this study highlights the need to assess different materials and methods of collection of biological samples, considering collection, extraction, and amplification.

Comparison of swab types for collection and analysis of microorganisms

The human microbiome has begun to emerge as a potential forensic tool, with varied applications ranging from unique identification to investigative leads that link individuals and/or locations. The relative abundance of the combined DNA of the microbiome, compared to human nuclear DNA, may expand potential sources of biological evidence, especially in cases with transfer or low-copy number DNA samples. This work sought to determine the optimal swab type for the collection and analysis of microorganisms. A bacterium (Proteus mirabilis) was deposited by pipette onto four swab types (cotton, flocked, dental applicators, and dissolvable), and extraction and real-time PCR quantitation of the bacterial DNA were performed, which allowed for absolute microbial DNA recovery and comparison of yields across the four sampling substrates. Flocked swabs had the highest yield (~1240 ng) compared to the cotton swabs (~184 ng), dental applicators (~533 ng), and dissolvable swabs (~430 ng). The collection efficiency was further evaluated for cotton and flocked swabs using dried microbial samples spotted onto non-porous surfaces (treated wood, glass, plastic, and tile). Flocked swabs performed consistently better across wood, glass, and tile, but showed decreased recovery from plastic. The cotton swabs failed in the recovery of P. mirabilis DNA across all surfaces. Knowing the appropriate sampling substrate will be useful as others continue to investigate the use of the microbiome as a forensics tool.

Comparison of Isohelix™ and Rayon swabbing systems for touch DNA recovery from metal surfaces

A previous study evaluating two swabbing systems found that DNA was best recovered from sterile metal substrates using an Isohelix™ swab wetted with isopropyl alcohol rather than a Rayon swab with water as the wetting agent. We tested the same swabbing systems on metal (aluminum, brass, and stainless steel) and plastic substrates in a regularly touched environment to simulate the non-deliberate transfer of touch evidence likely seen in a casework scenario, to ascertain the performance of these swabs in an uncontrolled situation. Higher amounts of touch DNA were recovered with Isohelix™ swabs (0.5 – 3.3 ng) compared to Rayon swabs (0.13 – 1.2 ng). The Isohelix™ swabbing system was found to significantly recover more touch DNA (p = 0.04) from the metal substrates than the Rayon swabbing system, consistent with the findings of our previous work. The results contribute to our understanding of the impact of sample collection techniques on touch DNA recovery from problematic metal surfaces and suggest that supplemental cleaning of substrates as a precautionary step against the spread of infections may affect touch DNA persistence and the recovery efficiency of swabs.

The correlation between the level of 3-hydroxypropyl mercapturic acid, CYP2B6 polymorphisms, and hematuria occurrences after cyclophosphamide administration and its bioanalytical methods: A systematic review

BACKGROUND

Cyclophosphamide (CPA) is a cytotoxic prodrug that needs to be metabolized by cytochrome P450 enzymes, like CYP2B6. Unfortunately, CYP2B6 is a very polymorphic enzyme and can cause a change in 3-hydroxypropyl mercapturic acid (3-HPMA), the most found CYP metabolite in urine levels. Change in 3-HPMA levels can also indicate the level change in its precursor, acrolein, which is responsible for the hematuria incidence after CPA administration.This review's purpose is to obtain a conclusion about the optimal 3-HPMA analysis method in urine after the administration of cyclophosphamide using liquid chromatography-tandem mass spectrometry (LC-MS/MS) through literature review from previous studies. Also, this review was written to examine the relationship between levels of 3-HPMA in urine, polymorphisms of CYP2B6 enzymes, and the incidence of hematuria after cyclophosphamide administration in cancer patients.

METHODS

Major databases, such as Universitas Indonesia's library database ScienceDirect, PubMed/Medline, Frontiers Media, and Google Scholar database, were used to find both published and unpublished studies without a time limit until 2020. Studies on pharmacokinetics, pharmacodynamics, drug therapy monitoring of cyclophosphamide, bioanalysis, and polymerase chain reaction (PCR) published in Indonesian and English were included. Meanwhile, non-related studies or studies written in other languages besides Indonesian and English were excluded. Two independent reviewers screened the titles, abstracts, and full-text manuscripts. Data obtained from eligible sources were used to answer the purpose of this review in a narrative form.

RESULTS

The authors found 436 related studies from various databases and websites. Then, the authors narrowed it down into 62 pieces of literature by removing the duplicates and reviewing the abstracts and full-text manuscripts. Out of 62 sources, the authors found 30 studies that explained 3-HPMA analysis using LC/MS-MS, CYP2B6 polymorphisms, and hematuria occurrences. The authors used those 30 studies to build a conclusion regarding the purpose of this study. We strengthened the results with some additional information from the other 32 eligible sources.

CONCLUSIONS

The authors conclude that according to literature searches from previous studies, the optimal 3-HPMA analysis method in urine after cyclophosphamide administration using LC-MS/MS is using triple quadrupole LC-MS/MS; source of positive ion electrospray ionization (ESI); mobile phase combination of 0.1% formic acid in water (A) - 0.1% formic acid in acetonitrile (90:10 v/v) (B); the Acquity® BEH C18 column (2.1 × 100 mm; 1.7 μm); injection volume of 10 μl; flow rate of 0.2 ml/minute; gradient elution method. Detection was carried out using mass spectrometry with m/z ratio of 222.10 > 90 for 3-HPMA and m/z 164.10 > 122 for n-acetylcysteine (NAC). The optimum sample preparation method is acidification and dilution ratio of 1:5 v/v. Also, there is a relationship between 3-HPMA levels, CYP2B6 polymorphisms, and the occurrences of hematuria after the administration of cyclophosphamide, which is a type of CYP2B6 polymorph, namely CYP2B6∗6, can increase cyclophosphamide hydroxylation so that it can increase the levels of acrolein and 3-HPMA, as its metabolites, and risk of hematuria.

ETHICS AND DISSEMINATION

This research does not use human participants, human data, or human tissue for being directly studied for the review. Therefore, ethics approval and consent to participate are not applicable.

REGISTRATION

This research has not been registered yet.

Innovative design of 3D-printed nasopharyngeal pediatric swab for COVID-19 detection

3-dimensional (3D) printing technology provides a solution to meet the high demand for producing adult nasal swabs. A smaller, more flexible nasopharyngeal swab needs to be developed for children and infants suspected of having coronavirus. The information shared here presents a novel 3D-printed pediatric swab for the purpose of collecting upper respiratory clinical specimens.

A comparison of cotton-tipped and nylon flocked swabs for culture of Neisseria gonorrhoeae from oropharyngeal samples

Our aim was to determine if there was a difference in culture positivity for oropharyngeal gonorrhoea when sampling using a nylon-flocked versus cotton-tipped swab. We collected FLOQSwabs and cotton-tipped swabs from individuals aged ≥ 18 years who had untreated oropharyngeal gonorrhoea detected by NAAT between November 2019-June 2020.Of 78 participants, 32 (41.0%) were culture-positive for N. gonorrhoeae from either swab. Of these 32, 29 (90.6%, 95%CI: 75.0%-98.0%) were positive on both swabs, one (3.1%, 95%CI: 0.0%-16.2%) tested positive on FLOQSwab only and two (6.2%, 95%CI: 0.1%-20.8%) tested positive on cotton-tipped swabs only. There was moderate agreement between the swabs in the amount of bacterial growth (Cohen's Kappa (k)=0.745; 95%CI: 0.622-0.868, p<0.001). Our results showed that the proportion of positive results was comparable using the FLOQSwabs versus the cotton-tipped swabs for oropharyngeal gonorrhoea culture.

A review of nasopharyngeal swab and saliva tests for SARS-CoV-2 infection: Disease timelines, relative sensitivities, and test optimization

Testing is an essential part of containment of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic. This review summarizes studies for SARS‐CoV‐2 infection and testing. Nasopharyngeal samples are best at sensitivity detection, especially in early stages of disease and in asymptomatic individuals. Current swab processing involves a 100‐ to 1000‐fold dilution of the patient sample. Future optimization of testing should focus on using smaller volumes of viral transport media and swab designs to increase comfort and increased viral adhesion.

Diagnostic performance and characteristics of anterior nasal collection for the SARS-CoV-2 antigen test: a prospective study

The clinical utility of antigen test using anterior nasal samples has not been well evaluated. We conducted a prospective study in a drive-through testing site located at a PCR center to evaluate the diagnostic performance of the antigen test QuickNavi-COVID19 Ag using anterior nasal samples and to compare the degrees of coughs or sneezes induction and the severity of pain between anterior nasal collection and nasopharyngeal collection. The study included a total of 862 participants, of which 91.6% were symptomatic. The median duration from symptom onset to sample collection was 2.0 days. Fifty-one participants tested positive for severe acute respiratory syndrome coronavirus 2 on reverse transcription PCR (RT-PCR) with nasopharyngeal samples, and all of them were symptomatic. In comparison to the findings of RT-PCR, the antigen test using anterior nasal samples showed 72.5% sensitivity (95% confidence interval [CI] 58.3-84.1%) and 100% specificity (95% CI 99.3-100%). Anterior nasal collection was associated with a significantly lower degree of coughs or sneezes induction and the severity of pain in comparison to nasopharyngeal collection (p < 0.001). The antigen test using anterior nasal samples showed moderate sensitivity in symptomatic patients who were at the early stages of the disease course but was less painful and induced fewer coughs or sneezes.

Identification of Genetic Variants in 65 Obesity Related Genes in a Cohort of Portuguese Obese Individuals

Obesity is a major public health problem, which has a strong genetic component that interplays with environmental factors. Several genes are known to be implicated in the regulation of body weight. The identification of alleles that can be associated with obesity is a key element to control this pandemic. On the basis of a Portuguese population, 65 obesity-related genes are sequenced using Next-Generation Sequencing (NGS) in 72 individuals with obesity, in order to identify variants associated with monogenic obesity and potential risk factors. A total of 429 variants are identified, 129 of which had already been associated with the phenotype. Comparing our results with the European and Global frequencies, from 1000 Genomes project, 23 potential risk variants are identified. Six new variants are discovered in heterozygous carriers: four missense (genes ALMS1-NM_015120.4:c.5552C>T; SORCS1-NM_001013031.2:c.1072A>G and NM_001013031.2: c.2491A>C; TMEM67-NM_153704.5:c.158A>G) and two synonymous (genes BBS1-NM_024649.4:c.1437C>T; TMEM67-NM_153704.5:c.2583T>C). Functional studies should be performed to validate these new findings and evaluate their penetrance and pathogenicity. Regardless of no cases of monogenic obesity being identified, this kind of investigational study is important when we are still trying to understand the aetiology and pathophysiology of obesity. This will allow the identification of rare variants associated with obesity and the study of their prevalence in specific populational groups.

Evidence Collection and Analysis for Touch Deoxyribonucleic Acid in Groping and Sexual Assault Cases

Historically, evidence collection in sexual assault cases focused on obtaining foreign contributor bodily fluids through swab collection. With improvements in deoxyribonucleic acid (DNA) analysis methods, DNA profiles can be developed from touch DNA and applied to sexual assault cases. Following a literature review on factors affecting touch DNA transfer, a groping case study with innovative evidence collection is presented to support the expansion of touch DNA evidence collection in sexual assault cases. The groping case led to the development of a statewide sexual assault touch DNA form to guide evidence collection. DNA findings from additional groping sexual assault cases are reported to further show and justify the importance of evidence collection in groping cases. Implications on multidisciplinary practices are summarized to promote evidence collection and analysis in groping sexual assault cases. As forensic nurses are educated to accurately collect DNA evidence and provide trauma-informed, patient-centered care, they are best suited to provide nursing care for patients who have experienced groping sexual assaults. Optimal DNA findings in groping and sexual assault cases are best achieved through development of strong multidisciplinary, collaborative relationships between forensic nurses and forensic scientists.

Enhanced forensic DNA recovery with appropriate swabs and optimized swabbing technique

Efficient sampling with swabs is crucial for optimal forensic DNA analysis. The DNA recovery is determined by the skill of the practitioner and the compatibility between the applied swab and the surface. Here we investigate the impact of swabbing technique and swab type on the DNA yield. Thirteen different swabs from four categories (cotton, flocked nylon, small foam and large foam) provided equal DNA yields for smooth/non-absorbing surfaces. Large foam swabs gave higher DNA recovery for an absorbing wood surface. Factorial design of experiments and ANOVA was applied to study swabbing techniques for cotton swabs. Two key factors for efficient sampling were found to be 1) holding the swab with an approximate 60° angle against the surface and 2) to rotate the swab during sampling. For absorbing wood, it was beneficial to wet the swab heavily. The results of the factorial experiments were used to develop swabbing protocols for different surfaces. When ten experienced practitioners sampled according to these protocols, the DNA yield was increased for ridged plastic (around 1.25 times more DNA) and absorbing wood (2.2-6.2 times more DNA). For window glass, representing a smooth/non-absorbing surface, sampling according to the protocol gave DNA yields equivalent to applying individual sampling techniques. The protocol lowered person-to-person variation for ridged plastic. In conclusion, we have developed instructive protocols for cotton swab sampling on three types of surfaces: smooth/non-absorbing, ridged/non-absorbing and smooth/absorbing. We believe that such swabbing protocols will streamline and simplify the training of new practitioners and improve sampling efficiency for invisible DNA residues in casework.

Ten years of molecular ballistics-a review and a field guide

Molecular ballistics combines molecular biological, forensic ballistic, and wound ballistic insights and approaches in the description, collection, objective investigation, and contextualization of the complex patterns of biological evidence that are generated by gunshots at biological targets. Setting out in 2010 with two seminal publications proving the principle that DNA from backspatter collected from inside surfaces of firearms can be retreived and successfully be analyzed, molecular ballistics covered a lot of ground until today. In this review, 10 years later, we begin with a comprehensive description and brief history of the field and lay out its intersections with other forensic disciplines like wound ballistics, forensic molecular biology, blood pattern analysis, and crime scene investigation. In an application guide section, we aim to raise consciousness to backspatter traces and the inside surfaces of firearms as sources of forensic evidence. Covering crime scene practical as well as forensic genetic aspects, we introduce operational requirements and lay out possible procedures, including forensic RNA analysis, when searching for, collecting, analyzing, and contextualizing such trace material. We discuss the intricacies and rationales of ballistic model building, employing different tissue, skin, and bone simulants and the advantages of the “triple-contrast” method in molecular ballistics and give advice on how to stage experimental shootings in molecular ballistic research. Finally, we take a look at future applications and prospects of molecular ballistics.

Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis

BACKGROUND

Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative. Nanopore sequencing technology is portable and capable of generating long sequencing reads in real-time. The aim of this study is to evaluate the potential of nanopore sequencing directly from clinical samples for the diagnosis of bacterial microbial keratitis.

METHODS

Using full-length 16S rRNA amplicon sequences from a defined mock microbial community, we evaluated and benchmarked our bioinformatics analysis pipeline for taxonomic assignment on three different 16S rRNA databases (NCBI 16S RefSeq, RDP and SILVA) with clustering at 97%, 99% and 100% similarities. Next, we optimised the sample collection using an ex vivo porcine model of microbial keratitis to compare DNA recovery rates of 12 different collection methods: 21-gauge needle, PTFE membrane (4 mm and 6 mm), Isohelix™ SK-2S, Sugi® Eyespear, Cotton, Rayon, Dryswab™, Hydraflock®, Albumin-coated, Purflock®, Purfoam and Polyester swabs. As a proof-of-concept study, we then used the sampling technique that provided the highest DNA recovery, along with the optimised bioinformatics pipeline, to prospectively collected samples from patients with suspected microbial keratitis. The resulting nanopore sequencing results were then compared to standard microbiology culture methods.

RESULTS

We found that applying alignment filtering to nanopore sequencing reads and aligning to the NCBI 16S RefSeq database at 100% similarity provided the most accurate bacterial taxa assignment. DNA concentration recovery rates differed significantly between the collection methods (p < 0.001), with the Sugi® Eyespear swab providing the highest mean rank of DNA concentration. Then, applying the optimised collection method and bioinformatics pipeline directly to samples from two patients with suspected microbial keratitis, sequencing results from Patient A were in agreement with culture results, whilst Patient B, with negative culture results and previous antibiotic use, showed agreement between nanopore and Illumina Miseq sequencing results.

CONCLUSION

We have optimised collection methods and demonstrated a novel workflow for identification of bacterial microbial keratitis using full-length 16S nanopore sequencing.

Ultra-absorptive Nanofiber Swabs for Improved Collection and Test Sensitivity of SARS-CoV-2 and other Biological Specimens

Following the COVID-19 outbreak, swabs for biological specimen collection were thrust to the forefront of healthcare materials. Swab sample collection and recovery are vital for reducing false negative diagnostic tests, early detection of pathogens, and harvesting DNA from limited biological samples. In this study, we report a new class of nanofiber swabs tipped with hierarchical 3D nanofiber objects produced by expanding electrospun membranes with a solids-of-revolution-inspired gas foaming technique. Nanofiber swabs significantly improve absorption and release of proteins, cells, bacteria, DNA, and viruses from solutions and surfaces. Implementation of nanofiber swabs in SARS-CoV-2 detection reduces the false negative rates at two viral concentrations and identifies SARS-CoV-2 at a 10× lower viral concentration compared to flocked and cotton swabs. The nanofiber swabs show great promise in improving test sensitivity, potentially leading to timely and accurate diagnosis of many diseases.

The effects of dithiothreitol (DTT) on fluorescent qPCR dyes

DNA extractions of semen samples commonly utilize dithiothreitol (DTT) to reduce and disrupt disulfide bonds. Although traditional extraction techniques remove DTT before downstream analyses, the forensic DNA community has recently explored Y-screening, direct amplification, and direct cell lysis assays that omit purification but employ reducing agents to lyse spermatozoa. This study examined the impact of residual DTT on downstream processes involving fluorescent dyes. Quantification using Investigator^® Quantiplex HYres revealed a significant increase in the male DNA yield (p = 0.00056) and a >150,000,000-fold increase in the male:human DNA ratio when DTT remained in extracts versus when it was filtered out using a traditional purification method. When DTT was present with Quantifiler™ Trio, the true mean DNA yield for the large autosomal target significantly increased (p = 0.038) and the average reported DNA yields increased 1.1-fold, >9.5-fold, and 1.3-fold for the small autosomal, large autosomal, and male targets, respectively. DTT-spiked DNA standards from both kits were impacted similarly to samples with residual DTT, demonstrating that observed effects were related to DTT and not the extraction method. This study corroborates other reports that DTT adversely affects multiple dyes (e.g., Cy5, Quasar 670, SYBR Green I, TMR, and Mustang Purple^® ). Overall, DTT causes inaccurate quantities and, consequently, inaccurate calculated male:female ratios when used in conjunction with these kits. Thus, implementation of newer direct-to-PCR assays incorporating DTT should either be avoided or used only with carefully evaluated, compatible dyes.

3D printing of nasopharyngeal swabs for COVID-19 diagnose: Past and current trends

The current technological advancements in emerging 3D printing technologies are indeed propitious. To date, ground-breaking 3D printing technologies are used in automobile, aerospace, clothing, pharma, and biomedical industries by creating pre-requisite engineered and tailored end-user products reaching standard sets. 3D printing is also becoming a crucial technology in support of enhanced health care and general emergency response since the beginning of the COVID-19 pandemic. As the world is facing a significant lack of medicinal supplies, manufactures are struggling to fulfill demands due to the ongoing COVID-19 pandemic. The decline in the diagnostic testing kits supply chained to increased interest in 3D printed Nasopharyngeal (NP) swabs. This article has reviewed and studied the sensitivity of the NP swabs and various NP swab designs. The process of different 3D printing technologies that are employed to address the swab shortages during COVID-19 is explained in detail. The paper ends with the conclusions drawn from the literature review.