Buccal Swabbing Research Articles

Salivary Transcriptome and Mitochondrial Analysis of Autism Spectrum Disorder Children Compared to Healthy Controls.

Autism rates have been reported to be increasing rapidly in industrialized societies. The pathology most often combines neurological symptoms associated with language and social impairments with gastrointestinal symptoms. This study aimed to measure differences in oral metatranscriptome and mitochondrial health between ASD children and neurotypical USA and Colombia ("Blue Zone") children. In addition, this study aimed to determine whether using prebiotics and probiotics would change the oral microbiome and mitochondrial health of ASD children. Buccal swabs and saliva samples were obtained from 30 autistic individuals (USA) at three intervals: prior to intervention, post-prebiotic, and post-probiotic. In addition, a subject component who were neurotypical, which included individuals from the USA (30) and Colombia (30), had buccal swabbing and salivary sampling performed for metatranscriptomic and mitochondrial comparison. Significant differences were observed in the temporal data, demonstrating shifts that interventions with probiotics and polyols may have precipitated. Particular bacterial strains were significantly more prevalent in the autism group, including a strain that reduced neurotransmitter levels via enzymatic degradation. This supports the hypothesis that the microbiome may influence the occurrence and degree of autism. Verbal skills increased in six of the 30 ASD subjects following xylitol and three more after probiotic supplementation, according to both parental reports and the subjects' healthcare providers.

Comparing skin swabs, buccal swabs, and toe clips for amphibian genetic sampling, a case study with a small anuran (Acris blanchardi).

Multiple methods for collecting genetic samples from amphibians exist, each with their own implications for study design, animal welfare, and costs. Toe clipping is one common method, but there is ongoing debate regarding its potential detriment. Less invasive methods should be implemented, if efficacious, as amphibians are a particularly vulnerable vertebrate group. Skin and buccal swabbing are less invasive methods for genetic sampling, but the potential for contamination and a lower yield of DNA may exist. To compare these methods, we gathered skin swabs, buccal swabs, and toe clips from the same individuals of a relatively small anuran species, Blanchard's Cricket Frog (Acris blanchardi). We then compared DNA yield, DNA purity, amplification success rate, and genotypic data quality among sample types. We found toe clips and buccal swabs generated similar DNA yield and purity, with skin swabs yielding significantly less DNA of significantly lower purity than the other sample types. Amplification success rate was significantly higher using toe clips compared to the other sample types, though buccal swab samples amplified more readily than skin swabs. Genotypic data from toe clips and buccal swabs did not differ significantly in quality, but skin swab data quality was significantly lowest among sample types. Thus, skin swabbing could produce erroneous data in some situations, but buccal swabbing is likely an effective substitute to toe clipping, even for small species. Our results can help future researchers select which genetic sampling method might best suit their research needs.

Successful DNA amplification of DNA from non-destructive buccal swabbing in Vespertilionid and Rhinolophid bats

AbstractAcquiring DNA from wild bats (Mammalia: Chiroptera) is typically undertaken utilizing highly invasive (but non-lethal) sampling techniques comprising wing biopsies and occasional blood samples. While non-invasive sampling is possible through the extraction of DNA from faecal samples, it is not always possible to acquire samples from individual bats whilst conducting fieldwork, and as such, this method is primarily applicable to roost occupancy identification. Similarly, wing swabbing is liable to cross-contamination from roost mates. Here we present the first use of oral (buccal) swabbing for successful, species-resolution DNA sequencing of Vespertilionidae and Rhinolophidae in 10 bat species (nine Vespertilionidae and one Rhinolophidae) from the UK.

Impact of Swabbing Location, Self-Swabbing, and Food Intake on SARS-CoV-2 RNA Detection.

This study compared SARS-CoV-2 RNA loads at different anatomical sites, and the impact of self-swabbing and food intake. Adult symptomatic patients with SARS-CoV-2 or non-SARS-CoV-2 respiratory tract infection were included between 2021 and 2022. Patients performed a nasal and buccal swab before a professionally collected nasopharyngeal/oropharyngeal swab (NOPS). Buccal swabs were collected fasting and after breakfast in a subgroup of patients. SARS-CoV-2 RNA loads were determined by nucleic acid testing. Swabbing convenience was evaluated using a survey. The median age of 199 patients was 54 years (interquartile range 38-68); 42% were female and 52% tested positive for SARS-CoV-2. The majority of patients (70%) were hospitalized. The mean SARS-CoV-2 RNA load was 6.6 log10 copies/mL (standard deviation (SD), ±1.5), 5.6 log10 copies/mL (SD ± 1.9), and 3.4 log10 copies/mL (SD ± 1.9) in the professionally collected NOPS, and self-collected nasal and buccal swabs, respectively (p < 0.0001). Sensitivity was 96.1% (95% CI 90.4-98.9) and 75.3% (95% CI 63.9-81.8) for the nasal and buccal swabs, respectively. After food intake, SARS-CoV-2 RNA load decreased (p = 0.0006). Buccal swabbing was the preferred sampling procedure for the patients. In conclusion, NOPS yielded the highest SARS-CoV-2 RNA loads. Nasal self-swabbing emerged as a reliable alternative in contrast to buccal swabs. If buccal swabs are used, they should be performed before food intake.

Comparing Genotyping Accuracy Using Buccal Swabs versus Tail Biopsies by PCR in B6;C3-Tg(Prnp-SNCA*A53T)83Vle and B6;C3-Tg(Prnp-SNCA*A53T)83Vle Sncatm1Mjff Mice.

Genotyping is a common and necessary procedure performed on genetically modified animals to distinguish carriers from noncarriers of the variants of interest. Established methods involve collection of tissues such as tips of tails or notches of ears. Noninvasive methods have been described but not widely adopted for reasons including inertia to change, needs to adjust PCR protocols, and the lack of validation; noninvasive genotyping methods are a refinement on animal welfare, but questions remain regarding how they compare with invasive methods in terms of genotyping accuracy rate and reproducibility. To gain answers to these questions, we compared the detection accuracy of the transgene and determination of zygosity in B6;C3-Tg(Prnp-SNCA*A53T)83Vle and B6;C3-Tg(Prnp-SNCA*A53T)83Vle Snca tm1Mjff neonatal mice between tail biopsies and buccal swabs. Moreover, we weighed and observed mice following genotyping to see if any clinical differences can be discerned. Weight data did not support statistically significant differences in mice undergoing different genotyping procedures and control. No statistically significant difference was found between using buccal swabs or tail biopsies for genotyping with PCR or quantitative PCR. None of the pups swabbed was rejected by the dam. Our findings indicate that buccal swabbing is a more humane and feasible alternative to tail biopsies for high-throughput genotyping.

The pros and cons of buccal swabbing and tail clipping for monitoring reptilian biodiversity

In biodiversity research, the retrieval of genetic material from organisms is a common and essential component for assessing genetic diversity. The welfare of the organism, however, needs to be balanced against the overall goal of the intended research. One sampling technique often applied to retrieve DNA material from small reptiles is the removal of a small portion of the distal end of the tail. While most squamate reptiles have tail autotomy, some species (e.g. many iguanid lizards and snakes) do not regenerate tail tissue. We therefore explored the efficacy of a minimally disruptive technique, buccal swabbing, as an alternative to tissue sampling via tail clipping, particularly for species without tail autotomy, using dwarf chameleons (Bradypodion spp.) as a case study. The two sampling techniques were compared to assess the efficacy of DNA retrieval. We also evaluated the financial implications of each technique. The results indicate that buccal swabs paired with a specialised DNA extraction kit offer a feasible (although expensive), once-off alternative to tissue sampling, but with no material left for biobanking. Deviations in swab type used and the DNA extraction process (i.e. using more affordable extraction procedures) resulted in poor DNA retrieval and unreadable sequences. This finding suggests that buccal swabbing can be a suitable alternative when finances are not constrained, an expensive extraction kit is available, and biobanking is not a concern. For researchers from low- to middle-income economies, this expensive alternative may hamper research progress by placing a financial obstacle in the way, and therefore the next best option is tissue sampling. Significance: This study provides guidance on the efficacy of buccal swabs as a viable alternative to tissue samples collected via tail clipping for DNA retrieval from small reptiles. The results indicate that swabs may be a feasible alternative to tissue samples when finances are not constrained. Deviations in buccal swabbing method (i.e. using more cost-effective alternatives) performed poorly in DNA retrieval and do not offer competitive alternatives to tissue samples. Although buccal swabs were shown to offer an alternative to tissue samples, the financial implications to research in low- to middle-income economies may hinder research goals unnecessarily.

DNA quality from buccal swabs in neonates: comparison of different storage time

BACKGROUND Genomic medicine has great potential for diagnoses, disease prediction, and targeted treatment. Buccal swabs are a suitable non-invasive method for neonates to obtain DNA samples. Due to Indonesia's geographical conditions, samples require a prolonged time to reach the genetic laboratory. This study aimed to compare the DNA quality of buccal swabs in neonates between immediate and after-storage extraction.&#x0D; METHODS This study was part of a study about the profile of human milk oligosaccharide and FUT2 genotype in Indonesian mother-infant dyads consisting of 20 neonates. 1 swab stick for each participant was taken using a standardized buccal swabbing protocol and divided into 2 isovolume aliquots, which were grouped into the immediate (extraction was performed within 3 days after sampling) and storage groups (extraction was performed on the 14th day after storage in 4°C). DNA yield and purity A260/280 ratio were measured by spectrophotometry. The PCR amplification and Sanger sequencing were performed to validate the DNA isolate quality for downstream application.&#x0D; RESULTS The DNA yield for the immediate group was similar compared with the storage group (9.50 [4.89] versus 9.10 [5.05] µg), p = 0.659, as well as DNA purity A260/280 (1.58 [0.24] versus 1.56 [0.28]), p = 0.785. PCR and sequencing of FUT2 results also showed similar quality between both groups.&#x0D; CONCLUSIONS The similar DNA quality and sequencing results between immediate and storage extraction confirmed that buccal swabs could be stored for 2 weeks, allowing ample time for sample shipping from remote areas to the laboratory.

The Role of Mycobacterium Tuberculosis Detection on Oral Mucosa in Diagnosis of Pulmonary Tuberculosis

Background. Tuberculosis is one of the world's health problems, with larger mortality rate than HIV/AIDS. In order to control this disease, a new and inexpensive diagnostic method is needed. Oral samples, such as buccal mucosa epithelium, can be an alternative specimen, other than sputum, in the diagnosis of tuberculosis. Purpose. This study aimed to analyze the presence of Mycobacterium tuberculosis on buccal swabbing of tuberculosis patients. Method. Study was conducted on 18 new pulmonary tuberculosis patients in TB DOTS unit of Dr. Soetomo General Hospital. Each subject was swabbed on the buccal mucosa of the oral cavity for subsequent examination of PCR, AFB, and culture to detect Mycobacterium tuberculosis in the oral cavity. Result. The results showed that Mycobacterium tuberculosis was detected from 2 study subjects (11%) using PCR, whereas in AFB and culture examination methods no Mycobacterium tuberculosis was detected on buccal mucosa of the oral cavity. Conclusion. This study showed that Mycobacterium tuberculosis was detected on buccal mucosa swab of tuberculosis patients based on PCR technique, but this method is less suitable in diagnosis of pulmonary tuberculosis.

Non-Lethal Detection of Ranavirus in Fish.

Emergent infectious diseases have an increasing impact on both farmed animals and wildlife. The ability to screen for pathogens is critical for understanding host-pathogen dynamics and informing better management. Ranavirus is a pathogen of concern, associated with disease outbreaks worldwide, affecting a broad range of fish, amphibian, and reptile hosts, but research has been limited. The traditional screening of internal tissues, such as the liver, has been regarded as the most effective for detecting and quantifying Ranavirus. However, such methodology imposes several limitations from ethical and conservation standpoints. Non-lethal sampling methods of viral detection were explored by comparing the efficacy of both buccal swabbing and fin clipping. The study was conducted on two Iberian, threatened freshwater fish (Iberochondrostoma lusitanicum and Cobitis paludica), and all samples were screened using qPCR. While for C. paludica both methods were reliable in detecting Ranavirus, on I. lusitanicum, there was a significantly higher detection rate in buccal swabs than in fin tissue. This study, therefore, reports that fin clipping may yield false Ranavirus negatives when in small-bodied freshwater fish. Overall, buccal swabbing is found to be good as an alternative to more invasive procedures, which is of extreme relevance, particularly when dealing with a threatened species.

Prospective evaluation of the clinical utility of whole-exome sequencing using buccal swabbing for undiagnosed rare diseases

Other SectionsAbstractIntroductionMaterials and MethodsResultsDiscussionSupplemental MaterialsConflict of interestAcknowledgementsAuthor’s ContributionsFigureTableReference

Non-Lethal Detection of Frog Virus 3-Like (RUK13) and Common Midwife Toad Virus-Like (PDE18) Ranaviruses in Two UK-Native Amphibian Species.

Ranaviruses have been involved in amphibian mass mortality events worldwide. Effective screening to control this pathogen is essential; however, current sampling methods are unsuitable for the detection of subclinical infections. Non-lethal screening is needed to prevent both further spread of ranavirus and losses of at-risk species. To assess non-lethal sampling methods, we conducted two experiments: bath exposing common frogs to RUK13 ranavirus at three concentrations, and exposing common toads to RUK13 or PDE18. Non-lethal sampling included buccal, digit, body and tank swabs, along with toe clips and stool taken across three time-points post-exposure. The presence/load of ranavirus was examined using quantitative PCR in 11 different tissues obtained from the same euthanised animals (incl. liver, gastro-intestinal tract and kidney). Buccal swab screening had the highest virus detection rate in both species (62% frogs; 71% toads) and produced consistently high virus levels compared to other non-lethal assays. The buccal swab was effective across multiple stages of infection and differing infection intensities, though low levels of infection were more difficult to detect. Buccal swab assays competed with, and even outperformed, lethal sampling in frogs and toads, respectively. Successful virus detection in the absence of clinical signs was observed (33% frogs; 50% toads); we found no difference in detectability for RUK13 and PDE18. Our results suggest that buccal swabbing could replace lethal sampling for screening and be introduced as standard practice for ranavirus surveillance.

Lateral flow test performance in children for SARS-CoV-2 using anterior nasal and buccal swabbing: sensitivity, specificity, negative and positive predictive values

ObjectiveTo determine if the sensitivity of the lateral flow test is dependent on the viral load and on the location of swabbing in the respiratory tract in children.DesignPhase 1: Routinely...

Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach.

Analysis of the cow microbiome, as well as host genetic influences on the establishment and colonization of the rumen microbiota, is critical for development of strategies to manipulate ruminal function toward more efficient and environmentally friendly milk production. To this end, the development and validation of noninvasive methods to sample the rumen microbiota at a large scale are required. In this study, we further optimized the analysis of buccal swab samples as a proxy for direct bacterial samples of the rumen of dairy cows. To identify an optimal time for sampling, we collected buccal swab and rumen samples at six different time points relative to animal feeding. We then evaluated several biases in these samples using a machine learning classifier (random forest) to select taxa that discriminate between buccal swab and rumen samples. Differences in the inverse Simpson's diversity, Shannon's evenness, and Bray-Curtis dissimilarities between methods were significantly less apparent when sampling was performed prior to morning feeding (P < 0.05), suggesting that this time point was optimal for representative sampling. In addition, the random forest classifier was able to accurately identify nonrumen taxa, including 10 oral and putative feed-associated taxa. Two highly prevalent (>60%) taxa in buccal and rumen samples had significant variance in relative abundances between sampling methods but could be qualitatively assessed via regular buccal swab sampling. This work not only provides new insights into the oral community of ruminants but also further validates and refines buccal swabbing as a method to assess the rumen bacterial in large herds.IMPORTANCE The gastrointestinal tracts of ruminants harbor a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health, and performance. While the influence of environmental factors on rumen microbes is well documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our inability to easily sample the rumen microbiota. There are three common methods for rumen sampling but all of them present at least one disadvantage, including animal welfare, sample quality, labor, and scalability. The development and validation of noninvasive methods, such as buccal swabbing, for large-scale rumen sampling is needed to support studies that require large sample sizes to generate reliable results. The validation of buccal swabbing will also support the development of molecular tools for the early diagnosis of metabolic disorders associated with microbial changes in large herds.

Validating buccal swabbing as a minimal-invasive method to detect pesticide exposure in squamate reptiles

The use of enzymatic biomarkers constitutes a widely used approach in ecotoxicology. However, standard sampling procedures are invasive, requiring tissue, organ or blood extraction. This leads to concerns regarding conservation practice, animal welfare and restrictions in study design. New techniques are needed to avoid these problems, but still generate reliable data. Here, we aimed at validating the use of buccal swabs as a reliable method to detect pesticide exposure in reptiles. Common wall lizards (Podarcis muralis) were divided into control, dermal and oral treatment groups and exposed to different pesticide formulations. Subsequently, buccal swabs were taken and enzymatic activity was analyzed. We were able to confirm the suitability of the method to detect effects of pesticide exposure on the enzymatic level. While exposure to the formulation Roundup Ultramax® didn't match when compared to effects previously observed in situ when compared to other glyphosate based formulations, effects could still be detected. This can be seen as a strong indicator that the active ingredient of a formulation may not always be the mian driver for ecotoxicological effectsat the enzymatic level. At the same time, exposure towards the single formulation Vivando® didn't result in any effects. However, individuals residing in agricultural landscapes will mostly be exposed to pesticide mixes containing different formulations. Our results strongly advocate that buccal swabbing is a reliable minimal invasive method to generate samples for detecting effects of pesticide exposure in reptiles. Due to its easy handling, we believe it will provide new opportunities concerning study designs.

Buccal swab: A tissue sampling method for refinement of experimental procedures involving rainbow trout

Summary Buccal swabbing is a minimally invasive method to obtain DNA and biological material from humans and animals, including fish. Reports on buccal swabbing in fish are few and only for a limited number of species. Rainbow trout (Oncorhynchus mykiss) is an important animal model and because the yield of DNA may vary among and within different species in individuals of different sizes, it was selected as useful to optimize the buccal DNA collection in this species. Different storage methods were evaluated, aimed at DNA preservation by limiting DNA degradation and bacterial growth, using commonly available and inexpensive reagents. DNA quality was also tested by amplification of a single-copy nuclear gene and a mitochondrial gene. The results suggest that ethanol is the best storage choice for buccal swab sampling in fish genetic studies, as well as suitable for small-bodied rainbow trout.

ACTN3 polymorphism prevalence in general population of six Balkan countries

The aim of this study was to investigate the prevalence of RR, RX and XX genotypes of rs1815739 single nucleotide polymorphism of ACTN3 gene in general population of six Balkan countries. This SNP is currently thought to give genetic predisposition for advantageous sport performance, with its R allele positively correlating with better performance in strength/power sports, and X allele being present in higher frequency in elite athletes in endurance disciplines. A total of 483 individuals (281 males and 202 females) from seven populations from six countries was tested. Samples were collected by buccal swabbing method, DNA was isolated according to salting-out protocol and genotyping was performed using PCR and RFLP analysis. Obtained results suggest that RR and RX genotypes (43.7% and 44.1%, respectively) are overrepresented when compared to XX genotype (12.2%). The XX genotype in the study samples is present in lower frequency when compared to the global (16-18%) and European (18%) average. This study reports the first population data on genotype prevalence in sports-related genes for this part of Europe and is the beginning of research interests that intend to investigate genetic predispositions of elite athletes from this region competing internationally in different disciplines.

Pros and cons of external swabbing of amphibians for genetic analyses

Non-invasive DNA sampling is an important tool in amphibian conservation. Buccal swabs are nowadays replacing the wounding toe-clipping method. Skin and cloaca swabbing are even less invasive and easier to handle than buccal swabbing, but could result in contaminations of genetic material. Therefore, we test if external skin and cloaca swabs are as reliable as buccal swabs for genetic analysis of amphibians. We analysed eight microsatellite loci for the common frog (Rana temporaria, Linnaeus 1758) and compared genotyping results for buccal, skin and cloaca swabs regarding allelic dropouts and false alleles. Furthermore, we compared two DNA extraction methods regarding efficiency and cost. DNA quality and quantity (amplification success, genotyping error rate, in nanogram per microlitre) were comparable among DNA sources and extraction methods. However, skin and cloaca samples exhibited high degrees of contamination with foreign individuals, which was due to sample collection during mating season. Here, we established a simple low budget procedure to receive DNA of amphibians avoiding stressful buccal swabbing or harmful toe clipping. However, the possibility of contaminations of external swabs has to be considered.

Buccal swabs as a reliable source of DNA for sexing young and adult Common Swifts (Apus apus)

We investigated the reliability of buccal swabs for molecular sex determination in very young nestlings (0-14 days old) and adults of the Common Swift (Apus apus) compared to the results from blood samples of the same individuals. Sex determination based on buccal swabs mat- ched the result of sex determination based on blood samples in 46 out of 47 nestlings (98 %) and in all 10 adults (100 %). Therefore, we consider that buccal swab sampling is a reliable noninvasive method to obtain DNA for sex determination in swifts. We recommend buccal swabbing as an alternative to blood sampling in future genetic studies in birds.

Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (Ichthyosaura alpestris)

This study introduces a novel DNA sampling method in amphibians using skin swabs. We assessed the relevancy of skin swabs relevancy for genetic studies by amplifying a set of 17 microsatellite markers in the alpine newt Ichthyosaura alpestris, including 14 new polymorphic loci, and a set of 11 microsatellite markers in Hyla arborea, from DNA collected with buccal swabs (the standard swab method), dorsal skin swabs and ventral skin swabs. We tested for quality and quantity of collected DNA with each method by comparing electrophoresis migration patterns. The consistency between genotypes obtained from skin swabs and buccal swabs was assessed. Dorsal swabs performed better than ventral swabs in both species, possibly due to differences in skin structure. Skin swabbing proved to be a useful alternative to buccal swabbing for small or vulnerable animals: by drastically limiting handling, this method may improve the trade-off between the scientific value of collected data, individual welfare and species conservation. In addition, the 14 new polymorphic microsatellites for the alpine newt will increase the power of genetic studies in this species. In four populations from France (n=19-25), the number of alleles per locus varied from 2 to 16 and expected heterozygosities ranged from 0.04 to 0.91. Presence of null alleles was detected in two markers and two pairs displayed gametic disequilibrium. No locus appeared to be sex-linked.

Description of microsatellite markers and genotyping performances using feathers and buccal swabs for the Ivory gull (Pagophila eburnea)

We report 22 new polymorphic microsatellites for the Ivory gull (Pagophila eburnea), and we describe how they can be efficiently co-amplified using multiplexed polymerase chain reactions. In addition, we report DNA concentration, amplification success, rates of genotyping errors and the number of genotyping repetitions required to obtain reliable data with three types of noninvasive or nondestructive samples: shed feathers collected in colonies, feathers plucked from living individuals and buccal swabs. In two populations from Greenland (n=21) and Russia (Severnaya Zemlya Archipelago, n=21), the number of alleles per locus varied between 2 and 17, and expected heterozygosity per population ranged from 0.18 to 0.92. Twenty of the markers conformed to Hardy-Weinberg and linkage equilibrium expectations. Most markers were easily amplified and highly reliable when analysed from buccal swabs and plucked feathers, showing that buccal swabbing is a very efficient approach allowing good quality DNA retrieval. Although DNA amplification success using single shed feathers was generally high, the genotypes obtained from this type of samples were prone to error and thus need to be amplified several times. The set of microsatellite markers described here together with multiplex amplification conditions and genotyping error rates will be useful for population genetic studies of the Ivory gull.