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Background: Microbiomics offers new methods for conducting epidemiological surveys of oral microbiota in large populations. Compared to curette sampling, swab sampling is more convenient and less technically sensitive, making it more suitable for such surveys. To verify the feasibility of using swabs for buccal mucosa sampling in large-scale studies, we collected samples from the buccal mucosa and tooth surfaces of healthy individuals using both swabs and curettes. Microbiomics was employed to analyze and compare microbial abundance and diversity between these two methods., Methods: Four sites were assessed: the buccal mucosa on both sides and the buccal surfaces of the left and right mandibular first molars. Two sampling methods, swab and curette, were used to collect bacterial communities from healthy individuals. Specifically, buccal mucosa samples (n = 10) and tooth surface samples (n = 20) were analyzed using 16 S rDNA gene sequencing. Bacterial signals were detected through fluorescence in situ hybridization (FISH), targeting the bacterial 16 S rDNA gene. Metastats analysis and Wilcoxon test were used., Results: A total of 383 OTUs were detected in the 30 samples, which belonged to 1 kingdom (bacteria), 11 phyla, 23 classes, 40 orders, 75 families, 143 genus, and 312 species. Among them, 223 OTUs were found on both the buccal mucosa and tooth surfaces. The statistics suggest that although there were no significant differences in colony composition, there were differences in the abundance and distribution of colonies on the dental and buccal mucosal surfaces. When detecting oral disease-causing pathogens such as Enterococcus faecalis and Porphyromonas gingivalis, the efficiency of detection is higher when using curette sampling. Compared to right tooth sampling with a curette, the swab sampling group had higher levels of Firmicutes, while Fusobacteria and Bacteroidetes were more prevalent in the curette tissues., Conclusions: In oral health individuals, there is no difference in the bacterial composition of the oral buccal mucosa and the dental surface, differing only in abundance. Thus, the buccal mucosa can act as a substitute for the teeth in epidemiological investigations exploring the bacterial composition of the oral cavity., (© 2024. The Author(s).)

Background: Tuberculosis (TB), a major cause of disease and antimicrobial resistance, is spread via aerosols. Aerosols have diagnostic potential and airborne-microbes other than Mycobacterium tuberculosis complex (MTBC) may influence transmission. We evaluated whether PneumoniaCheck (PMC), a commercial aerosol collection device, captures MTBC and the aeromicrobiome of people with TB., Methods: PMC was done in sputum culture-positive people (≥ 30 forced coughs each, n = 16) pre-treatment and PMC air reservoir (bag, corresponding to upper airways) and filter (lower airways) washes underwent Xpert MTB/RIF Ultra (Ultra) and 16S rRNA gene sequencing (sequencing also done on sputum). In a subset (n = 6), PMC microbiota (bag, filter) was compared to oral washes and bronchoalveolar lavage fluid (BALF)., Findings: 54% (7/13) bags and 46% (6/14) filters were Ultra-positive. Sequencing read counts and microbial diversity did not differ across bags, filters, and sputum. However, microbial composition in bags (Sphingobium-, Corynebacterium-, Novosphingobium-enriched) and filters (Mycobacterium-, Sphingobium-, Corynebacterium-enriched) each differed vs. sputum. Furthermore, sequencing only detected Mycobacterium in bags and filters but not sputum. In the subset, bag and filter microbial diversity did not differ vs. oral washes or BALF but microbial composition differed. Bags vs. BALF were Sphingobium-enriched and Mycobacterium-, Streptococcus-, and Anaerosinus-depleted (Anaerosinus also depleted in filters vs. BALF). Compared to BALF, none of the aerosol-enriched taxa were enriched in oral washes or sputum., Interpretation: PMC captures aerosols with Ultra-detectable MTBC and MTBC is more detectable in aerosols than sputum by sequencing. The aeromicrobiome is distinct from sputum, oral washes and BALF and contains differentially-enriched lower respiratory tract microbes., (© 2024. The Author(s).)

The maternal pregnancy microbiome (including genitourinary and gut) has been linked to important pregnancy/birth and later childhood health outcomes. However, such sampling as part of large population cohort studies is logistically and financially challenging. Many countries routinely collect vaginal or vaginal-rectal swabs in late pregnancy for Group B Streptococcus (GBS) screening, but their utility for population-based research is still unclear. As part of planning for the Generation Victoria population-based cohort study beginning in pregnancy, we assessed the utility and reliability of residual clinical GBS vaginal/vaginal-rectal swabs for generating late pregnancy microbiome data. We carried out a two-phased pilot study. Phase one assessed the level of microbial diversity apparent in 'residual' clinical vaginal/vaginal-rectal swabs post clinical testing and storage for 7-10 days at 4 °C (routine clinical practice). Phase two directly assessed the impact of storage time and temperature on the microbial composition of vaginal/vaginal-rectal swabs collected specifically for research purposes. The microbiota composition in the 'residual' clinical swabs aligned with published studies. The 'research' swabs, stored at 4 °C for up to ten days, showed minimal changes in microbiota profile, compared to swabs examined on the day of collection. In contrast, significant variation in diversity was seen in swabs stored at room temperature for up to 48 h. Residual clinical material from swabs collected primarily for GBS screening in late pregnancy represent a reliable and abundant source of material for assessing the late pregnancy maternal microbiome for research purposes. This represents a low-burden opportunity for population-representative pregnancy studies to assess the potential of late pregnancy microbiome for prediction and understanding maternal and child health outcomes., (© 2024. Crown.)

Introduction: Mass screening for SARS-CoV-2 using nasopharyngeal swabs (NPS) is costly, uncomfortable for patients, and increases the chance of virus exposure to health care workers. Therefore, this study focused on determining if self-collected unpreserved saliva can be an effective alternative to NPS collection in COVID-19 surveillance., Materials and Methods: In this study, patients being tested for SARS-CoV-2 using NPS were asked to provide a saliva sample to compare their results. NPS samples were evaluated for SARS-CoV-2 using BioFire® FilmArray® Torch® or Cepheid® GeneXpert® systems while saliva samples were evaluated using an in-house developed reverse transcriptase polymerase chain reaction (RT-PCR) which targeted the Envelope (E) and Nucleocapsid (N) genes., Results: Detection of SARS-CoV-2 using self-collected saliva was found to be only slightly less accurate (<5%) than testing using NPS. In addition, initial saliva RT-PCR identified 27 positive subjects, 18 of which provided amplicons sufficient for confirmatory sequencing. The sequencing data showed a genetic shift in the virus within our population sometime between 22 June and July 8, 2021 from Alpha to Delta variant., Conclusions: The saliva sample collection method identifies the E gene in SARS COVID-2 samples which provides an alternative specimen source to the NPS. This identifies the S gene and ORF1ab. Saliva collection is more convenient to the patient, yields comparable results to NPS collection, and potentially increases Covid-19 surveillance., (Published by Oxford University Press on behalf of the Association of Military Surgeons of the United States 2024. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

ObjectivesWe evaluated how storing vaginal samples at room temperature in stabilising solutions versus immediate freezing affects 16S rRNA gene amplicon sequencing-based microbiota studies, aiming to simplify home and field collection., Methods: Twenty participants self-collected six mid-vaginal swabs that were stored in two nucleic acid preservatives (three in modified Solution C2 (Qiagen) and three in Amies/RNALater (Sigma)) in January-February 2016. From each set, two were immediately frozen (-80°C) and one was shipped to the University of Idaho (Moscow, Idaho) with return shipping to the Institute for Genome Sciences (Baltimore, Maryland). Amplicon sequencing of the 16S rRNA gene was used to characterise the vaginal microbiota, VALENCIA was used to assign community state types (CSTs), and quantitative PCR (qPCR) of 16S rRNA genes was used to estimate bacterial abundance. Cohen's Kappa statistic was used to assess within-participant agreement. Bayesian difference of means models assessed within-participant comparisons between shipped and immediately frozen samples., Results: There were 115 samples available for analysis. Average duration of transit for shipped samples was 8 days (SD: 1.60, range: 6-11). Within-participant comparisons of CSTs between shipped and immediately frozen samples revealed complete concordance (kappa: 1.0) for both preservative solutions. No significant differences comparing shipped and immediately frozen samples were found with taxon-level comparisons or bacterial abundances based on pan-bacterial qPCR., Conclusions: Short-term room temperature shipping of vaginal swabs placed in stabilising solutions did not affect vaginal microbiota composition. Home collection with mail-in of vaginal samples may be a reasonable approach for research and clinical purposes to assess the vaginal microbiota., Competing Interests: Competing interests: JR is co-founder of LUCA Biologics, a biotechnology company focusing on translating microbiome research into live biotherapeutics drugs. ST has been a consultant for Biofire Diagnostics, Roche Molecular Diagnostics and Luca Biologics, receives royalties from UPTODATE and has received speaker honoraria from Roche Molecular Diagnostics and Medscape/WebMD. ST, KG, RB and JR participate in research supported by in-kind donation of test kits by Hologic. JH has been a consultant for Intralytix Inc. LJF consults with Psomagen, Inc. to evaluate factors that influence the outcome of in vitro fertilisation., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: The rapid transmission and high pathogenicity of respiratory viruses significantly impact the health of both children and adults. Extracting and detecting their nucleic acid is crucial for disease prevention and treatment strategies. However, current extraction methods are laborious and time-consuming and show significant variations in nucleic acid content and purity among different kits, affecting detection sensitivity and efficiency. Our aim is to develop a novel method that reduces extraction time, simplifies operational steps, and ensures high-quality acquisition of respiratory viral nucleic acid., Methods: We extracted respiratory syncytial virus (RSV) nucleic acid using reagents with different components and analyzed cycle threshold (Ct) values via quantitative real-time polymerase chain reaction (qRT-PCR) to optimize and validate the novel lysis and washing solution. The performance of this method was compared against magnetic bead, spin column, and precipitation methods for extracting nucleic acid from various respiratory viruses. The clinical utility of this method was confirmed by comparing it to the standard magnetic bead method for extracting clinical specimens of influenza A virus (IAV)., Results: The solution, composed of equal parts glycerin and ethanol (50% each), offers an innovative washing approach that achieved comparable efficacy to conventional methods in a single abbreviated cycle. When combined with our A Plus lysis solution, our novel five-minute nucleic acid extraction (FME) method for respiratory viruses yielded superior RNA concentrations and purity compared to traditional methods. FME, when used with a universal automatic nucleic acid extractor, demonstrated similar efficiency as various conventional methods in analyzing diverse concentrations of respiratory viruses. In detecting respiratory specimens from 525 patients suspected of IAV infection, the FME method showed an equivalent detection rate to the standard magnetic bead method, with a total coincidence rate of 95.43% and a kappa statistic of 0.901 (P < 0.001)., Conclusions: The FME developed in this study enables the rapid and efficient extraction of nucleic acid from respiratory samples, laying a crucial foundation for the implementation of expedited molecular diagnosis., (© 2024. The Author(s).)

In this study, we aimed to assess the feasibility of re-collecting breath samples using the Centri® (Markes International, Bridgend, UK) followed by two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS) analysis. The work was conducted in two main phases. In the first phase, we evaluated the re-collection performance by analyzing two sets of standards, including a Grob mix primary solution and a standard mixture of 20 selected volatile compounds (VCs) covering different classes of organic species commonly found in breath samples. The intra-day and inter-day precision (reported as relative standard deviation (RSD),%) for the re-collection of the Grob mix primary solution were in the range of 1 % to14 % and 3 % to12 %, respectively. The re-collection accuracy ranged from 78 % to 97 %. The intra-day RSD for the re-collection of the standard mixture of selected VCs was within 20 % for all compounds, except for acetone and nonane. The precision was within 25 % for all compounds, except for nonane, n-hexane, 1,4-dichlorobenzene, and decane, which exhibited less than 36 % RSD. The re-collection accuracy was in the range of 67 % to 129 %. In the second phase of the study, the re-collection performance in breath analysis was evaluated via five repetitive splitting and re-collection of six breath samples obtained from healthy adults, realizing a total of 30 breath analyses. Initially, we evaluated the re-collection performance by considering all features obtained from breath analysis and then focused on the 20 VCs commonly found in breath samples. The re-collection accuracy for total breath features ranged from 86 to 103 %, and the RSDs were in the range of 1.0 % to 10.4 %. For the selected VCs, the re-collection accuracy of all compounds, except for undecane and benzene, was in the range of 71 % to 132 %., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Background: Specimens with incorrect patient information are both a critical safety error and difficult to identify. Estimates of sample mislabelling rely on subjective identification of mislabelling, with the possibility that not all mislabelled samples are being caught., Methods: We determined the blood type of two or more complete blood count specimens with the same patient label and assessed for discrepancies. We additionally determined the rate of identified sample mislabelling for the study period., Results: We found a rate of 3.17 per 1000 discrepancies over the study period. These discrepancies most likely represent occult, or unidentified, mislabelled samples. In contrast, the rate of identified sample mislabelling was 1.15 per 1000., Conclusions: This study suggests that specimens identified as, or known to be, mislabelled represent only a fraction of those mislabelled. These findings are currently being confirmed in our laboratory and are likely generalisable to other institutions., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)

Osteosarcoma and Ewing sarcoma are bone tumors mostly diagnosed in children, adolescents, and young adults. Despite multimodal therapy, morbidity is high and survival rates remain low, especially in the metastatic disease setting. Trials investigating targeted therapies and immunotherapies have not been groundbreaking. Better understanding of biological subgroups, the role of the tumor immune microenvironment, factors that promote metastasis, and clinical biomarkers of prognosis and drug response are required to make progress. A prerequisite to achieve desired success is a thorough, systematic, and clinically linked biological analysis of patient samples, but disease rarity and tissue processing challenges such as logistics and infrastructure have contributed to a lack of relevant samples for clinical care and research. There is a need for a Europe-wide framework to be implemented for the adequate and minimal sampling, processing, storage, and analysis of patient samples. Two international panels of scientists, clinicians, and patient and parent advocates have formed the Fight Osteosarcoma Through European Research consortium and the Euro Ewing Consortium. The consortia shared their expertise and institutional practices to formulate new guidelines. We report new reference standards for adequate and minimally required sampling (time points, diagnostic samples, and liquid biopsy tubes), handling, and biobanking to enable advanced biological studies in bone sarcoma. We describe standards for analysis and annotation to drive collaboration and data harmonization with practical, legal, and ethical considerations. This position paper provides comprehensive guidelines that should become the new standards of care that will accelerate scientific progress, promote collaboration, and improve outcomes., (©2024 The Authors; Published by the American Association for Cancer Research.)

Introduction: Primary Human Papilloma Virus (HPV) testing offers higher sensitivity and specificity over Visual Inspection using Acetic acid (VIA) in cervical cancer screening. Self-sampling is a promising strategy to boost participation and reduce disparities. However, concerns about the initial costs hinder HPV testing adoption in low and middle-income countries. This study assesses the cost-utility of home-based HPV self-sampling versus VIA for cervical cancer screening in India., Methods: A cross-sectional study was conducted in East district, Sikkim, India, comparing the costs and utility outcomes of population-based cervical cancer screening through VIA and primary HPV screening through self-sampling. Cost-related data were collected from April 2021 to March 2022 using the bottom-up micro-costing method, while utility measures were collected prospectively using the EuroQoL-5D-5L questionnaire. The utility values were converted into quality-adjusted life days (QALDs) for an 8-day period. The willingness to pay threshold (WTP) was based on per capita GDP for 2022. If the calculated Incremental Cost-Effectiveness Ratio (ICER) value is lower than the WTP threshold, it signifies that the intervention is cost-effective., Results: The study included 95 women in each group of cervical cancer screening with VIA & HPV self-sampling. For eight days, the QALD was found to be 7.977 for the VIA group and 8.0 for the HPV group. The unit cost per woman screened by VIA and HPV self-testing was ₹1,597 (US$ 19.2) and ₹1,271(US$ 15.3), respectively. The ICER was ₹-14,459 (US$ -173.6), which was much below the WTP threshold for eight QALDs, i.e. ₹ 4,193 (US$ 50.4)., Conclusion: The findings support HPV self-sampling as a cost-effective alternative to VIA. This informs policymakers and healthcare providers for better resource allocation in cervical cancer screening in Sikkim., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Hariprasad et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Polymeric bags are a widely applied, simple, and cost-effective method for the storage and offline analysis of gaseous samples. Various materials have been used as sampling bags, all known to contain impurities and differing in their cost, durability, and storage capabilities. Herein, we present a comparative study of several well-known bag materials, Tedlar (PVF), Kynar (PVDF), Teflon (PTFE), and Nalophan (PET), as well as a new material, ethylene vinyl copolymer (EVOH), commonly used for storing food. We investigated the influences of storage conditions, humidity, bag cleaning, and light exposure on volatile organic compound concentration (acetone, acetic acid, isoprene, benzene, limonene, among others) in samples of exhaled human breath stored in bags for up to 48 h. Specifically, we show high losses of short-chain fatty acids (SCFAs) in bags of all materials (for most SCFAs, less than 50% after 8 h of storage). We found that samples in Tedlar, Nalophan, and EVOH bags undergo changes in composition when exposed to UV radiation over a period of 48 h. We report high initial impurity levels in all the bags and their doubling after a period of 48 h. We compare secondary electrospray ionization and proton transfer reaction mass spectrometry in the context of offline analysis after storage in sampling bags. We provide an analytical perspective on the temporal evolution of bag contents by presenting the intensity changes of all significant m / z features. We also present a simple, automated, and cost-effective offline sample introduction system, which enables controlled delivery of collected gaseous samples from polymeric bags into the mass spectrometer. Overall, our findings suggest that sampling bags exhibit high levels of impurities, are sensitive to several environmental factors (e.g. light exposure), and provide low recoveries for some classes of compounds, e.g. SCFAs., (Creative Commons Attribution license.)

Volume electron microscopy encompasses a set of electron microscopy techniques that can be used to examine the ultrastructure of biological tissues and cells in three dimensions. Two block face techniques, focused ion beam scanning electron microscopy (FIB-SEM) and serial block face scanning electron microscopy (SBF-SEM) have often been used to study biological tissue samples. More recently, these techniques have been adapted to in vitro tissue culture samples. Here we describe step-by-step protocols for two sample embedding methods for in vitro tissue culture cells intended to be studied using SBF-SEM. The first focuses on cell pellet embedding and the second on en face embedding. En face embedding can be combined with light microscopy, and this CLEM workflow can be used to identify specific biological events by light microscopy, which can then be imaged using SBF-SEM. We systematically outline the steps necessary to fix, stain, embed and image adherent tissue culture cell monolayers by SBF-SEM. In addition to sample preparation, we discuss optimization of parameters for data collection. We highlight the challenges and key steps of sample preparation, and the consideration of imaging variables., Competing Interests: The authors have declared that no competing interests exist, (Copyright: © 2024 Antao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Microbiota analyses are key to understanding the bacterial communities within dairy cattle, but the impact of different storage conditions on these analyses remains unclear. This study sought to examine the effects of freezing at -80°C immediately after collection, refrigeration at 4°C for three days and seven days and absolute ethanol preservation on the microbiota diversity of pooled fecal samples from dairy cattle. Examining 16S rRNA gene sequences, alpha (Shannon, Pielou evenness, observed features and Faith PD indices) and beta (Bray-Curtis, βw and Weighted UniFrac) diversity were assessed. The effects of storage conditions on these metrics were evaluated using linear mixed models and PERMANOVA, incorporating the farm as a random effect. Our findings reveal that 7d and E significantly altered the Shannon index, suggesting a change in community composition. Changes in Pielou evenness for 3d and 7d storage when compared to 0d were found, indicating a shift in species evenness. Ethanol preservation impacted both observed features and Faith PD indices. Storage conditions significantly influenced Bray-Curtis, βw, and Weighted UniFrac metrics, indicating changes in community structure. PERMANOVA analysis showed that these storage conditions significantly contributed to microbiota differences compared to immediate freezing. In conclusion, our results demonstrate that while refrigeration for three days had minimal impact, seven days of refrigeration and ethanol preservation significantly altered microbiota analyses. These findings highlight the importance of sample storage considerations in microbiota research., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Jaramillo-Jaramillo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Transbronchial cryobiopsy is a promising technique for biopsy of peripheral pulmonary lesions (PPL). However, cryobiopsy specimen retrieval can pose problems due to the risk of bleeding during the blind period when the bronchoscope and cryoprobe are removed en bloc. Artificial airways and prophylactic balloon placement are risk-reducing measures, but the latter is challenging in upper lobe PPL. Specimen retrieval through standard guide sheath (GS) system without the need for bronchoscope removal may now be feasible with the ultrathin cryoprobe., Methods: Retrospective review of radial endobronchial ultrasound (rEBUS)-guided transbronchial cryobiopsy for PPL cases in which cryobiopsy specimen was retrieved through the GS over a 6-month period., Results: Twenty patients were included with an overall median age of 66.50 (IQR: 53.0 to 76.7). The median procedural time was 30 (IQR: 25.0 to 33.7) minutes. Median target size was 3.20 (IQR: 2.17 to 4.84) cm with 85% of lesions demonstrated "within" rEBUS orientation. Overall technical feasibility was 85% with median cryoactivation of 4.0 (IQR: 3.0 to 4.0) seconds. No specimen was retrieved in 3 patients. The diagnostic yield for forceps and cryobiopsy was 70% and 60%, respectively, and the combined diagnostic yield was 85% (P<0.01 vs. forceps biopsy). Median aggregate size for forceps and cryobiopsy was 8.0 (IQR: 5.3 to 10.0) and 4.5 (IQR: 2.3 to 7.0) mm respectively (P<0.01). No pneumothorax was reported and mild self-limiting bleeding was encountered in 30% of cases., Conclusion: Retrieval of cryoprobe through standard GS appears to be a safe and feasible method that can simplify the transbronchial cryobiopsy procedure and complement forceps biopsy in specific cases., Competing Interests: Disclosure: There is no conflict of interest or other disclosures., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

Biobanks have become an integral part of health and bioscience research. However, the ultra-low temperature (ULT) storage methods that biobanks employ [ULT freezers and liquid nitrogen (LN2)] are associated with carbon emissions that contribute to anthropogenic climate change. This paper aims to provide a 'Roadmap' for reducing carbon emissions associated with ULT storage in biobanking. The Roadmap offers recommendations associated with nine areas of ULT storage practice: four relating to ULT freezers, three associated with LN2 storage, and two generalised discussions regarding biosample management and centralisation. For each practice, we describe (a) the best approaches to mitigate carbon emissions, (b) explore barriers associated with hindering their implementation, and (c) make a series of recommendations that can help biobank stakeholders overcome these barriers. The recommendations were the output of a one year, UK-based, multidisciplinary research project that involved a quantitative Carbon Footprinting Assessment of the emissions associated with 1 year of ULT storage (for both freezers and LN2) at four different case study sites; as well as two follow up stakeholder workshops to qualitatively explore UK biobank stakeholder perceptions, views, and experiences on how to consider such assessments within the broader social, political, financial, technical, and cultural contexts of biobanking., (© 2024. The Author(s).)

Gel lubrication is routinely used during gynecological examination to prevent or reduce pain, yet its impact on microbial composition during sampling remains unclear. This study aimed to investigate whether lubricating gel affects the microbial composition of vaginal samples. We included 31 pregnant women presenting during their third trimester to clinics or emergency room and collected 143 unique vaginal samples for 16S amplicon microbial analysis. Vaginal samples were obtained using sterile swabs under various conditions: without gel-immediately frozen (n = 30), with gel-immediately frozen, without gel-at room temperature (RT) for 5 h before freezing, with gel-at RT for 5 h before freezing, and additional sampling after 24 h without gel-immediate freezing. We found that sample collection with gel lubrication influenced specimen quality-half of the gel samples failing to meet processing limitation compared to those without gel. The effect of gel on testing quality dissipated after 24 h. However, when samples met post-sequencing filters, gel lubrication did not alter the microbial composition, individual taxa abundance or alpha and beta diversity. We recommend sampling either before gel exposure or 24 h after. These findings underscore the importance of considering sample collection methodologies in vaginal microbiome studies to ensure high-quality microbial data for accurate analysis., (© 2024. The Author(s).)

Esophageal cancer (EC) is a multifaceted disease. Our understanding of the involvement of esophageal microbiota in its pathogenesis and progression is limited, which is due to the lack of proper endoscopic sampling methods. Hereby, we conducted a comparative analysis of paired samples obtained through endoscopic brushing and cytosponge, aiming at assessing the feasibility of using cytosponge as a minimally invasive sampling way for studying esophageal microbiota. Our findings suggest that cytosponge sampling yielded significantly superior community richness and diversity compared to endoscopic brushing in both controls (non-cancerous) and EC individuals. The analysis of beta-diversity revealed distinct microbial community pattern in the genus diversity between the two sampling methods, underscoring the importance of selecting appropriate sampling methods to effectively characterize the esophageal microbiota. Specifically, Lactococcus and Serratia showed higher abundance in the samples collected by endoscopic brushing, while Alloprevotella and Leptotrichia were more enriched in the samples collected by cytosponge. These differences in dominant microbes were associated with metabolic pathways that particularly were related to host inflammation, such as pyruvate and glucose metabolisms. Notably, the phylogenetic levels of the microbiota indicated varied explanatory power for different detection purposes. This study underscores the substantial impact of sampling method selection on the acquisition of esophageal microbiota associated with the EC development, encompassing considerations of both abundance and diversity. This highlights the significance of selecting an appropriate sampling method for investigating the esophageal microbial status and studying the micro-environment in EC-related individuals., Importance: This study addresses a critical issue in esophageal cancer study by comparing two different sampling methods, endoscopic brushing and cytosponge, for investigating the esophageal microbiota. Our work highlights the suitability of the cytosponge technique as a minimally invasive sampling method for studying the esophageal microbiota and emphasizes the importance of selecting an appropriate sampling method to characterize the microbial community. Our findings have significant implications for advancing the understanding of the role of the esophageal microbiota in cancer development and will inform future research and clinical approaches in this field., Competing Interests: The authors declare no conflict of interest.

Aims: The optimal sampling methods for detecting human papillomavirus (HPV) in male genital sites remain unclear. This study aimed to assess the performance, acceptability, and comfort of two sampling techniques for male genital HPV detection., Methods and Results: A total of 490 men aged 18-45 were randomly assigned in a 1:1 ratio to undergo either the rub-brush (nail file followed by swab) or brush-only method (swab only) for sampling at external genitalia sites (PGS) and perineum/perianal (PA) sites. HPV distribution, specimen validity (β-globin as a quality reference), and participant acceptability and comfort were evaluated between the two sampling methods. The brush-only method demonstrated non-inferiority in detecting 14 high-risk HPV types (16/18/31/33/35/39/45/51/52/56/58/59/66/68) compared to the rub-brush method in both PGS (18.9% vs. 16.9%) and PA (10.5% vs. 11.9%). Although no significant differences were observed in positive rates for other HPV types, the brush-only method had a significantly higher invalid rate in PA (8.5% vs. 1.5%). Approximately 85.0% of participants reported good acceptability and comfort with both sampling methods, regardless of anatomical sites., Conclusions: This study suggests comparable performance, acceptability and comfort between the two sampling techniques for HPV detection. However, the rub-brush method may offer an advantage in higher sample validity., (© The Author(s) 2024. Published by Oxford University Press on behalf of Applied Microbiology International.)

Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon analysis, and paleoproteomic analysis to provide information on diet, dating, taxonomy, and phylogeny. Current paleoproteomic methods are destructive and require from a few milligrams to several tens of milligrams of bone for analysis. In many cultures, bones are raw materials for artifacts that are conserved in museums, which hampers damage to these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy, and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape discs for sampling. The sampled bone micropowders were digested following our highly optimized enhanced filter-aided sample preparation protocol and then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be carried out at archeological sites or in museums.

Triacylglycerols and wax esters are two lipid classes that have been linked to diseases, including autism, Alzheimer's disease, dementia, cardiovascular disease, dry eye disease, and diabetes, and thus are molecules worthy of biomarker exploration studies. Since triacylglycerols and wax esters make up the majority of skin-surface lipid secretions, a viable sampling method for these potential biomarkers would be that of groomed latent fingerprints. Currently, however, blood-based sampling protocols predominate in the field. The invasiveness of a blood draw limits its utility to protected populations, including children and the elderly. Herein we describe a noninvasive means for sample collection (from fingerprints) paired with fast MS data-acquisition (MassIVE data set MSV000092742) and efficient data analysis via machine learning. Using both supervised and unsupervised classification, we demonstrate the usefulness of this method in determining whether a variable of interest imparts measurable change within the lipidomic data set. As a proof-of-concept, we show that the method is capable of distinguishing between the fingerprints of different individuals as well as between anatomical sebum collection regions. This noninvasive, high-throughput approach enables future lipidomic biomarker researchers to more easily include underrepresented, protected populations, such as children and the elderly, thus moving the field closer to definitive disease diagnoses that apply to all.

Background: Latinas experience the greatest cervical cancer incidence compared with other ethnic/racial groups in the United States (US) due in part to significant disparities in screening uptake. Social and structural conditions that impede access to and participation in screening include language barriers, concerns about documentation status, logistical issues (e.g., transportation, limited clinic hours), and cultural beliefs regarding modesty and promiscuity. To overcome these challenges, self-sampling for human papillomavirus (HPV) DNA testing has emerged as a potentially promising method for promoting cervical cancer screening among this population. Thus, this systematic review aimed to assess the acceptability of HPV self-sampling among US Latinas., Methods: Using EBSCOhost and PubMed databases, we searched for studies published in the past two decades (2003-2023) that described participation in HPV self-sampling among Latinas. Eleven articles met inclusion criteria., Results: The majority of studies were conducted in Florida, California, and Puerto Rico, were single-arm designs, and involved the use of community health workers and Spanish-language materials (e.g., brochures). Across studies, the majority of participants reported that self-sampling was acceptable with respect to ease of use, comfort (lack of pain), privacy, and convenience; however, some women were concerned about the accuracy of self-sampling or whether they had performed sample collection correctly., Conclusion: Given the high acceptability, self-collection of cervicovaginal samples for HPV testing may offer a feasible option for enhancing participation in cervical cancer screening in this population that encounters significant barriers to screening., (© 2024 The Author(s). Cancer Medicine published by John Wiley & Sons Ltd.)

Finding out about sample preparation and transportation of structural biology samples in Acta Crystallographica F, Structural Biology Communications.

Background: Skin cancer specimen handling in Australian histopathology laboratories, while largely standardised, exhibits significant variations that affect clinical decision-making and patient outcomes., Objective: This article provides clinicians with an understanding of histopathological processes to enhance diagnostic precision, inform surgical margin evaluations and refine management approaches., Discussion: Understanding specimen handling and protocols is vital for accurate interpretation of pathology reports and management of skin cancers. Variations in sampling, examination and sectioning can affect pathological diagnosis and margin assessment. Clinician insights into laboratory processes are crucial for best practice. Retention of specimens and reports allows for further evaluation if clinical circumstances evolve or additional investigations are required.

Background: The GeneXpert MTB/RIF (Xpert) assay is a widely used technology for detecting Mycobacterium tuberculosis (MTB) in clinical samples. However, the study on the failure of the Xpert assay during routine implementation and its potential solutions is limited., Methods: We retrospectively analyzed the records of unsuccessful tests in the Xpert and the GeneXpert MTB/RIF Ultra (Ultra) assays between April 2017 and April 2021 at the Shanghai Public Health Clinical Center. To further investigate the effect of prolonged preprocessing on clinical sputum, an additional 120 sputum samples were collected for Xpert testing after 15 min, 3 h, and 6 h preprocessing. The analysis was performed by SPSS version 19.0 software., Results: A total of 11,314 test records were analyzed, of which 268 (2.37%) had unsuccessful test results. Among these, 221 (1.95%) were reported as "Error", 43 (0.38%) as "Invalid", and 4 (0.04%) as "No result". The most common clinical specimen for Xpert tests was sputum, accounting for 114 (2.17%) unsuccessful tests. The failure rate of urine specimens was lower than that of sputum (OR = 0.12, 95% CI: 0.02-0.88, χ 2  = 6.22, p = 0.021). In contrast, the failure rate of stool specimens was approximately twice as high as that of sputum (OR = 1.93, 95% CI: 1.09-3.40, χ 2  = 5.35, p = 0.014). In the prolonged preprocessing experiment, 102 cases (85%) yielded consistent results in Xpert tests. Furthermore, 7 cases (5.83%) detected an increase in MTB load, 8 cases (6.67%) detected a decrease in MTB load, and 3 cases (2.5%) yielded incongruent results in MTB and rifampicin resistance detection., Conclusions: The primary cause of unsuccessful tests in the Xpert assay was reported as "Error". Despite varying failure rates depending on the samples, the Xpert assay can be applied to extrapulmonary samples. For paucibacillary specimens, retesting the remaining preprocessed mixture should be carefully considered., (© 2024. The Author(s).)

The composition of human skin microbiome profoundly impacts host skin health and disease. However, the relationship between skin homeostasis or the development of skin diseases and daily changes in skin microbial composition is poorly understood. Longitudinal samplings at more frequent intervals would address this issue, while conventional sampling methods have technical difficulties, leading to limitations in sampling opportunities. Here, we developed a simple and stable tape-stripping method regardless of the operator's skill. Our method enables skin microbial sampling within 30 seconds and taking multiple skin microbial samples from the same body site. The amount of microbial DNA among multiple sampling sites could be measured within 13.5%. The sequencing results of multiple sampling showed high consistency, Pearson's correlation coefficient between multiple samples of 0.98. Furthermore, these results were comparable to those collected by the conventional swabbing method. These results demonstrate that our tape-stripping method enables simple microbiome collection and highly reliable quantitative skin microbiome analysis. These features of our method would lead to a further understanding of skin disease development or diagnosis of skin conditions in clinical research by increasing the opportunities for microbial sampling., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Preparation of biomacromolecules for structural biology studies is a complex and time-consuming process. The goal is to produce a highly concentrated, highly pure product that is often shipped to large facilities with tools to prepare the samples for crystallization trials or for measurements at synchrotrons and cryoEM centers. The aim of this article is to provide guidance and to discuss general considerations for shipping biomacromolecular samples. Details are also provided about shipping samples for specific experiment types, including solution- and cryogenic-based techniques. These guidelines are provided with the hope that the time and energy invested in sample preparation is not lost due to shipping logistics., (open access.)

Background: We assessed experiences of human papillomavirus (HPV) vaginal self-sampling and future screening preferences in an ethnically and socio-economically diverse group of women overdue for cervical screening., Setting and Participants: A postal questionnaire was embedded in the YouScreen self-sampling trial in England: 32.5% (2712/8338) of kit completers returned the survey. Kit non-completers were encouraged to return a questionnaire, but no responses were received. Participants were ethnically diverse (40.3% came from ethnic minority backgrounds), and 59.1% came from the two most deprived quintiles. Differences in confidence in kit completion, trust in the test results and intention to attend a follow-up test if HPV-positive were evaluated using Pearson's χ 2 analyses. Binary logistic regression models explored predictors of a future screening choice and preferences for urine versus vaginal self-sampling., Results: Most kit-completers reported high confidence in self-sampling (82.6%) and high trust in the results (79.9%), but experiences varied by ethnicity and screening status. Most free-text comments were positive but some reported difficulties using the device, pain or discomfort. Most women would opt for self-sampling in the future (71.3% vs. 10.4% for a clinician-taken test) and it was more often preferred by ethnic minority groups, overdue screeners and never attenders. Urine self-tests were preferred to vaginal tests (41.9% vs. 15.4%), especially among women from Asian, Black or Other Ethnic backgrounds., Conclusions: Kit-completers were confident, found the test easy to complete, and trusted the self-sample results. However, experiences varied by ethnic group and some women highlighted difficulties with the kit. Most women would prefer self-sampling in the future, but it was not a universal preference, so offering a choice will be important., Patient or Public Contribution: We did not have direct patient and public involvement and engagement (PPIE) in the questionnaire design. However, patients and public representatives did input into the design of the YouScreen trial and reviewed the wider study materials (e.g. participant information sheet)., Trial Registration: This questionnaire study was embedded in the YouScreen trial. The protocol for the YouScreen trial is available at https://www.isrctn.com/ISRCTN12759467. The National Institute for Health Research 43 Clinical Research Network (NIHR CRN) Central Portfolio Management System (CPMS) ID is 4441934., (© 2024 The Author(s). Health Expectations published by John Wiley & Sons Ltd.)

Environmental DNA (eDNA) analyses of species present in marine environments is the most effective biological diversity measurement tool currently available. eDNA sampling methods are an intrinsically important part of the eDNA biodiversity analysis process. Identification and development of eDNA sampling methods that are as rapid, affordable, versatile and practical as possible will improve rates of detection of marine species. Optimal outcomes of eDNA biodiversity surveys come from studies employing high levels of sampling replication, so any methods that make sampling faster and cheaper will improve scientific outcomes. eDNA sampling methods that can be applied more widely will also enable sampling from a greater range of marine surface micro-habitats, resulting in detection of a wider range of organisms. In this study, we compared diversity detection by several methods for sampling eDNA from submerged marine surfaces: polyurethane foam, nylon swabs, microfibre paint rollers, and sediment scoops. All of the methods produced a diverse range of species identifications, with >250 multicellular species represented by eDNA at the study site. We found that widely-available small paint rollers were an effective, readily available and affordable method for sampling eDNA from underwater marine surfaces. This approach enables the sampling of marine eDNA using extended poles, or potentially by remotely operated vehicles, where surface sampling by hand is impractical., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Michael Marnane reports a relationship with Chevron Energy Technology Co that includes: employment. Euan S Harvey reports a relationship with Chevron Energy Technology Co that includes: funding grants. Jason B Alexander reports financial support, article publishing charges, equipment, drugs, or supplies, and writing assistance were provided by Chevron Energy Technology Co. Travis Elsdon reports a relationship with Chevron Energy Technology Co that includes: employment. Sherralee S Lukehurst reports a relationship with BHP Group Ltd. that includes: funding grants. Simon Jarman reports a relationship with Chevron Energy Technology Co that includes: funding grants., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

DNA retrieval methods traditionally used during forensic evidence recovery including swabbing and tape lifting, can have limited effectiveness when used on porous, rough substrates such as bricks and carpet. This is possibly due to the DNA material being dispersed and unreachable for surface sampling techniques. In this evaluation we investigated the effectiveness of the Microbial Wet-Vacuum System (M-Vac®; M-Vac® Systems, Inc., Sandy, UT), as it has been reported to retrieve greater amounts of DNA material from challenging exhibits. A four-stage evaluation was conducted, starting with seeding carpet and brick substrates with a known donor's saliva in two dilutions and comparing the DNA recovery of tape lifting, swabbing, and the M-Vac®. A victim struggle scenario on carpet was then mimicked to compare trace DNA recovery by each method. Two mock scenarios were also conducted; a shirt was submerged in a creek bed for a period of five days to sample for the wearer's DNA, and a car boot was sampled to assess the possibility of recovering a victim's DNA amongst background DNA from the usual car occupants. Finally, the compatibility of the M-Vac® sampling process was optimised for the fully automated DNA lysis and extraction platforms used in the NSW (Australia) jurisdiction by comparing filter subsampling methods. The results from the study were mixed. For bricks, none of the collection methods were effective in retrieving DNA. On carpet, the M-Vac® retrieved the greatest quantities of DNA from the saliva-seeded samples, however, tape lifts outperformed all methods for 'touch' DNA recovery. The M-Vac® retrieved the greatest amount of DNA from the t-shirt recovered from a creek bed as it was able to retrieve the embedded DNA. The final mock case car boot scenario resulted in greater victim DNA recovery from tape lifts, with the M-Vac® more likely to recover mixtures too weak and/or complex to be interpreted. Finally, operational considerations regarding the compatibility of the M-Vac® system with fully automated DNA lysis and extraction are discussed. Considering the substantial time and cost to deploy the M-Vac®, it is recommended to be utilised in casework only after swabbing and tape lifting methods have failed to yield sufficient DNA material, where the substrate properties would likely benefit from the M-Vac's® niche capabilities for retrieving embedded DNA, and low levels of background DNA may be anticipated., Competing Interests: Declaration of Competing Interest None., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Criminals often attempt to conceal blood-stained weapons used in violent crimes, making forensic evidence crucial in solving cases. This study explores the recovery and extraction of trace DNA from sports equipment, including cricket bats, table tennis racquets, and hockey sticks, which are frequently implicated in such incidents. Our research evaluates various double swab collection methods for retrieving trace DNA from these sports items, emphasizing those associated with blunt force trauma. We also compare presumptive and confirmatory tests to establish a direct correlation. This research consistently demonstrated robust DNA recovery, surpassing a 50 % threshold across all tests. Specifically, DNA recovery from buried samples reached an impressive 87 %, while washed samples still yielded a substantial 80 % efficiency. We conducted a comparative analysis between presumptive and confirmatory testing methods, establishing a direct correlation between the two. Variability in DNA recovery efficiency was observed and attributed to factors like the type of surface the items contacted, and ambient humidity levels. In addition to presenting robust DNA recovery rates, statistical analyses were employed to compare methods, establishing correlations and highlighting the influence of environmental factors on DNA recovery efficiency. These findings have significant implications for forensic investigations involving silent weapons crafted from sports equipment, emphasizing the need for standardized protocols and consideration of environmental factors in DNA analysis., Competing Interests: Conflict of interest All authors declare there is no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Collecting and preserving biological samples in the field, particularly in remote areas in tropical forests, prior to laboratory analysis is challenging. Blood samples in many cases are used for nucleic acid-based species determination, genomics or pathogen research. In most cases, maintaining a cold chain is impossible and samples remain at ambient temperature for extended periods of time before controlled storage conditions become available. Dried blood spot (DBS) storage, blood stored on cellulose-based paper, has been widely applied to facilitate sample collection and preservation in the field for decades. However, it is unclear how long-term storage on this substrate affects nucleic acid concentration and integrity. We analysed nucleic acid quality from DBS stored on Whatman filter paper no. 3 and FTA cards for up to 15 years in comparison to cold-chain stored samples using four nucleic acid extraction methods. We examined the ability to identify viral sequences from samples of 12 free-ranging primates in the Amazon forest, using targeted hybridization capture, and determined if mitochondrial genomes could be retrieved. The results suggest that even after extended periods of storage, DBS will be suitable for some genomic applications but may be of limited use for viral pathogen research, particularly RNA viruses., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Background and Aims: Pancreatic juice cytology is useful for diagnosing pancreatic duct strictures and cystic lesions. However, some cases cannot be diagnosed using cytology. This study aimed to evaluate the utility of the overnight-stored pancreatic juice cell block (CB) method for diagnosing pancreatic disease., Methods: This retrospective study included 32 patients who presented with pancreatic duct strictures or cystic lesions between 2018 and 2024. The sensitivity, specificity, and accuracy of the CB method and single/multiple pancreatic juice cytology were compared to evaluate the utility of the CB., Result: An endoscopic nasopancreatic drainage tube was placed in the main pancreatic duct, and pancreatic juice was collected to create a CB specimen. The median amount of pancreatic juice collected was 180(30-200) mL, and the median number of cytological examinations was three(2-8). Of the 32 cases, 13 were malignant, and 19 were benign (non-malignant). The sensitivity was significantly higher for the CB method (62 %) than for single cytology(15 %, P = 0.0414), and there was no significant difference between CB and multiple cytology(54 %, P = 1.0). The specificity and accuracy were not significantly different between the CB method and single or multiple cytology. When multiple cytology and CB were combined, sensitivity improved to 77 %. The pathological findings of the CB specimens were similar to the surgical specimens, including immunohistochemistry., Conclusion: The overnight-stored pancreatic juice CB method was more effective than single cytology, with similar sensitivities to multiple cytology and can also be used for immunohistochemistry. The pancreatic juice CB method is useful for pancreatic juice assessment., (Copyright © 2024 IAP and EPC. Published by Elsevier B.V. All rights reserved.)

The isolation of Campylobacter fetus subsp. venerealis (Cfv) from clinical samples is the gold standard for confirming cases of bovine genital campylobacteriosis, an important cause of infertility in cattle and a potential public health concern. Furthermore, isolation is also necessary for the development of autologous vaccines, characterization of strains for antimicrobial susceptibility patterns, etc. Nevertheless, the sensitivity of culture methods is usually low, and there is no standardized protocol to maximize the recovery of Cfv from clinical samples. The aim of the current study is to design a protocol for the culture of Cfv from preputial samples by evaluating the combination of different transport, enrichment and culture media considering the impact of certain factors (time between collection and enrichment, temperature, and use of filters). The use of modified Lander's transport medium and storing the sample for 24 h at 21 ± 2 °C led to the highest recovery of Cfv CFUs. In contrast, the storage of the samples during 24-48 h in PBS and Thomann rarely allowed the recovery of Cfv regardless of the temperature. The enrichment medium yielding the best results was Preston (significantly higher recovery than Brucella medium), while Cfv could not be isolated with Bolton. Regarding our diagnostic assay (using Lander as transport medium and Preston as enrichment medium), the best protocol in terms of maximizing Cfv recovery as well as limiting contaminations is to culture the samples in i) solid media Preston or Skirrow, and ii) using 0.65 μm filters and incubating plates at 37 °C in microaerophilic conditions., (© 2024. The Author(s).)

Along with the recent acknowledgement of the World Anti-Doping Agency to use dried blood spot (DBS) samples for routine doping control purposes, there have been propositions to use DBS as a matrix that allows regular proactive remotely supervised self-sampling, providing potential longitudinal monitoring of an athlete's exposure to doping agents. However, several organizational aspects have to be considered before implementation, such as the verification of the sample collections time point. Based on a previous untargeted proteomics workflow utilizing liquid chromatography-high-resolution mass spectrometry (LC-HRMS) to identify protein/peptide markers to define the time since deposition of a bloodstain, the aim of the current study was to develop a targeted LC-HRMS/MS analytical method for promising peptidic target analytes. A long-term DBS storage experiment was carried out over a 3-month period (sample collection time points: 0, 2, 4, 7, 14, 21, 28, 42, 56, 70, 84 and 91 days) with DBS samples of 10 volunteers for longitudinal investigation of signal abundance changes of targeted peptide sequences at different storage temperatures (room temperature [RT], 4°C and -20°C). Prior to experimental analysis, LC-HRMS/MS method characteristics were successfully assessed, including intraday precision, carryover and sample extract stability. For estimation of DBS sample collection time points, ratios of two peptides that originate from the same protein prior to tryptic digestion were created. Two targeted peptide area ratios were found to significantly increase after being stored at RT for 28 days, representing potential markers for future use in routine doping controls that contribute to advancing complementary avenues in anti-doping., (© 2023 The Authors. Drug Testing and Analysis published by John Wiley & Sons Ltd.)

Background: Group B streptococcus (GBS) is a bacterium carried by 20-25 % of pregnant women in the UK, which can be transmitted from pregnant women to their babies at the time of birth. Women can be tested for GBS in pregnancy using a vaginal-rectal swab, however, this testing is currently not routinely offered in the UK. A large clinical trial is underway to determine the clinical and cost-effectiveness of routine testing (ISRCTN reference number ISRCTN49639731). A crucial part of understanding whether this type of test should be implemented is women's views on the acceptability of being offered GBS tests, their preferences towards testing procedures and their willingness to receive these tests., Aim: To explore women's views on the acceptability of different methods of Group B streptococcal bacteria (GBS) testing in pregnancy, including self-swabbing procedures., Methods: A convenience sample of 19 women (5 pregnant and 14 postpartum) were interviewed using a semi-structured interview guide. Interviews were transcribed and analysed using systematic thematic analysis., Results: Findings show that many of the women interviewed were not concerned about being offered a GBS test, were willing to provide a sample and felt positive towards samples being taken to detect GBS. Women varied in their preferences on the best time for sampling. Some thought being approached during pregnancy gave them time to understand the purpose of testing, prepare for what may happen next and ask questions about potential treatment if needed. Others thought labour was a good time to provide accurate results on GBS carriage at birth and reduce unnecessary worry during pregnancy. However, women were concerned that they may be unable to make an informed decision in labour due to time, pain and the prospect of birthing quickly. Women perceived clinician swabbing as more accurate than self-sampling; however, many thought clinician swabbing might be embarrassing so self-swabs should be available to increase uptake for some women., Conclusions: Overall, women thought both pregnancy and labour were acceptable times to test for GBS. The majority found both clinician and self-swabbing procedures acceptable; however, many had a preferred swabbing option and thought women should be given the choice of the swabbing procedure most acceptable to them. It is important that women are given information about GBS testing and its procedures in pregnancy regardless of when the GBS swabbing is performed., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2024. Published by Elsevier Ltd.)

Previous studies have shown that environmental DNA (eDNA) from human sources can be recovered from natural bodies of water, and the generation of DNA profiles from such environmental samples may assist in forensic investigations. However, fundamental knowledge gaps exist around the factors influencing the probability of detecting human eDNA and the design of optimal sampling protocols. One of these is understanding the particle sizes eDNA signals are most strongly associated with and the most appropriate filter size needed for efficiently capturing eDNA particles. This study assessed the amount of mitochondrial eDNA associated with different particle sizes from human blood and skin cells recovered from freshwater samples. Samples (300 mL) were taken from experimental 10 L tanks of freshwater spiked with 50 µL of human blood or skin cells deposited by vigorously rubbing hands together for two minutes in freshwater. Subsamples were collected by passing 250 mL of experimental water sample through six different filter pore sizes (from 0.1 to 8 µm). This process was repeated at four time intervals after spiking over 72 hours to assess if the particle size of the amount of eDNA recovered changes as the eDNA degrades. Using a human-specific quantitative polymerase chain reaction (qPCR) assay targeting the HV1 mitochondrial gene region, the total amount of mitochondrial eDNA associated with different particle size fractions was determined. In the case of human blood, at 0 h, the 0.45 µm filter pore size captured the greatest amount of mitochondrial eDNA, capturing 42 % of the eDNA detected. The pattern then changed after 48 h, with the 5 µm filter pore size capturing the greatest amount of eDNA (67 %), and 81 % of eDNA at 72 h. Notably, a ten-fold dilution proved to be a valuable strategy for enhancing eDNA recovery from the 8 µm filter at all time points, primarily due to the PCR inhibition observed in hemoglobin. For human skin cells, the greatest amounts of eDNA were recovered from the 8 µm filter pore size and were consistent through time (capturing 37 %, 56 %, and 88 % of eDNA at 0 hours, 48 hours, and 72 hours respectively). There is a clear variation in the amount of eDNA recovered between different cell types, and in some forensic scenarios, there is likely to be a mix of cell types present. These results suggest it would be best to use a 5 µm filter pore size to capture human blood and an 8 µm filter pore size to capture human skin cells to maximize DNA recovery from freshwater samples. Depending on the cell type contributing to the eDNA, a combination of different filter pore sizes may be employed to optimize the recovery of human DNA from water samples. This study provides the groundwork for optimizing a strategy for the efficient recovery of human eDNA from aquatic environments, paving the way for its broader application in forensic and environmental sciences., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: We aimed to evaluate how urine chemistry tests are impacted by collection using a female external urinary catheter employing wicking and suction, to assess this catheter's potential as an alternative to transurethral catheters for collecting urine samples from incontinent patients., Methods: We obtained 50 random 40 mL refrigerated urine specimens from excess volume submitted to the Michigan Medicine Biochemical Laboratory. Specimens were split into a 10 mL "control" sample simulating voided urine, and a 30 mL paired "wicked" sample applied dropwise to and collected from a fresh PureWick system simulating collection from an incontinent patient. Each sample pair was tested for glucose, sodium, potassium, creatinine, urea, total protein, and derived ratios of sodium/creatinine, urea/creatinine, and protein/creatinine, then compared using Pearson correlation coefficients. Wicking materials were imaged via absorption contrast tomography on a laboratory X-ray microscope, to study the structure through which urine passes., Results: Control and wicked urine samples had very similar results for all chemical tests evaluated: strong Pearson correlation coefficients ranging from 0.955 (potassium) to 0.997 (glucose). Microscopic assessment of the amorphous wicking materials demonstrated an average pore spacing of 95.38 µm., Conclusions: Common urine chemistry tests were unaltered by collection using the PureWick female external catheter system. This external device can be used to collect urine for chemistry tests as an alternative to transurethral catheters., (Published by Elsevier Inc.)

Purpose: In April 2020, the UK Government implemented NHS Test and Trace to provide SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (qRT-PCR) testing for the public, with nose-and-throat swabbing for samples performed by trained staff. Self-swabbing (SS) would allow rapid scale-up of testing capacity and access. Six studies were undertaken to determine whether SS was as effective for detecting SARS-CoV-2 as swabbing performed by trained staff., Methods: Six prospective studies were conducted between April-October 2020, using six swab/media combinations. Differences between assisted swabbing (AS) and SS were evaluated for concordance, positivity, sensitivity, cycle threshold (Ct) values and void rates. Statistical analysis was performed using 95% confidence intervals (CIs), paired t-tests and model-based methods., Results: Overall, 3,253 individuals were recruited (median age 37 years, 49% female), with 2,933 having valid paired qRT-PCR results. Pooled concordance rate was 98% (95% CI: 96%, 99%). Positivity rate differences for SS (8.1%) and AS (8.4%) and differences in pooled sensitivities between SS (86%; 95% CI: 78%, 92%) and AS (91%; 95% CI: 78%, 96%) were nonsignificant. Both types of swabbing led to pooled void rates below 2% and strongly correlated Ct values. Age, sex and previous swabbing experience did not have a significant impact on concordance or sensitivity., Conclusion: The UK adopted a policy to promote self-testing for SARS-CoV-2 based on data demonstrating equivalence of SS versus AS. Positive outcomes with SS are likely generalisable to testing for other respiratory pathogens, and we consider self-sampling and self-testing essential for future pandemic preparedness., (© 2024. Crown.)

Recent studies highlight the presence of bacterial sequences in the human blood, suggesting potential clinical significance for circulating microbial signatures. These sequences could presumably serve in the diagnosis, prediction, or monitoring of various health conditions. Ensuring the similarity of samples before bacterial analysis is crucial, especially when combining samples from different biobanks prepared under varying conditions (such as different DNA extraction kits, centrifugation conditions, blood collection tubes, etc.). In this study, we aimed to analyze the impact of different sample collection and nucleic acid extraction criteria (blood collection tube, centrifugation, input volume, and DNA extraction kit) on circulating bacterial composition. Blood samples from four healthy individuals were collected into three different sample collection tubes: K2EDTA plasma tube, sodium citrate plasma tube, and gel tube for blood serum. Tubes were centrifugated at standard and double centrifugation conditions. DNA extraction was performed using 100, 200, and 500 μL plasma/serum input volumes. DNA extraction was performed using three different isolation kits: Norgen plasma/serum cell-free circulating DNA purification micro kit, Applied Biosystems MagMAX cell-free DNA isolation kit, and Qiagen QIAamp MinElute cell-free circulating DNA mini kit. All samples were subjected to 16S rRNA V1-V2 library preparation and sequencing. In total, 216 DNA and 18 water control samples were included in the study. According to PERMANOVA, PCoA, Mann-Whitney, and FDR tests the effect of the DNA extraction kit on the microbiota composition was the greatest, whereas the type of blood collection tube, centrifugation type, and sample input volume for the extraction had minor effects. Samples extracted with the Norgen DNA extraction kit were enriched with Gram-negative bacteria, whereas samples extracted with the Qiagen and MagMAX kits were enriched with Gram-positive bacteria. Bacterial profiles of samples prepared with the Qiagen and MagMAX DNA extraction kits were more similar, whereas samples prepared with the Norgen DNA extraction kit were significantly different from other groups.

The purpose of this study was to investigate the feasibility and effectiveness of COVID-19 throat swab samples delivered by medical drones in epidemic prevention and control. This study was carried out in both southern and northern hospital districts of the Affiliated Hospital of Jiangnan University from May to October 2022. The main participants were the Affiliated Hospital of Jiangnan University and Zhejiang Antwork Technology Co., Ltd. We first constructed an urban medical unmanned aerial vehicle (UAV) delivery system and developed a UAV-specific storage box for COVID-19 samples. The UAV system was used to transport COVID-19 throat swab samples from the northern hospital district to the southern hospital district, and the following indexes were obtained: (1) flight time of COVID-19 samples delivered by UAV, (2) real-time temperature of COVID-19 nucleic acid samples during transportation, and (3) the time of distribution of COVID-19 nucleic acid samples by road traffic as measured using the Baidu Maps application, compared with the flight time of UAV. The COVID-19 sample delivery system for urban medical UAV mainly consists of intelligent logistics UAV, low-temperature COVID-19 throat swab sample storage box, unmanned logistics hub, and cloud operation control platform. The flight distance between the northern and southern districts of the Affiliated Hospital of Jiangnan University was 10 km, and the ground distance was 24 km. From May 11 to October 28, 2022, a total of 1,190 UAV flights occurred. The average flight time was 13 minutes, which was 40 to 70 minutes faster than the average road travel time required for manual delivery of COVID-19 throat swab samples. At different time points in the day, UAV delivery efficiency increased by 67.5% to 82%. The use of 5G with the Internet of Things and UAV technology to deliver nucleic acid samples has the characteristics of fast speed, being unaffected by ground traffic conditions, and the ability to ensure the safety of nucleic acid samples in the transportation process, which is worthy of further study.

Introduction: The accuracy of urine culture results can be affected by pre-analytical factors such as transport delays and storage conditions. The objectives of this study were to analyze urine collection practices and assess the impact of introducing boric acid tubes for urine collection on quantitative urinary bacterial cultures of hospitalized patients in medical wards., Methods: A quasi-experimental pre-post study conducted in an acute care facility. In the pre-intervention phase (2020-2021), urine samples were transported without preservatives at room temperature. In 2022 (post-intervention), we transitioned to boric acid transport tubes, evaluating its effect on significant bacterial growth (≥ 105 CFU/ml). Bivariate and multivariate analyses identified predictors of culture positivity., Results: Throughout the duration of the study, a total of 12,660 urine cultures were analyzed. Date and time documentation was complete for 38.3% of specimens. Culture positivity was higher with longer processing times: positivity was 21.3% (220/1034) when specimens were processed within 4 h, 28.4% (955/3364) when processed in 4-24 h, and 32.9% (137/417) when processed after 24 h (p < 0.0001). For 4-24-hour processing, positivity decreased from 30.4% (704/2317) pre-intervention to 24.0% (251/1047) post-intervention (p < 0.001), with no significant changes in < 4 or ≥ 24-hour specimens. Stratified analysis by processing time revealed that the intervention was associated with reduced positivity only in cultures processed within 4-24 h (OR 0.80, 95% CI 0.67-0.94; p = 0.008)., Conclusion: The introduction of boric acid transport tubes predominantly influenced cultures transported within a 4-24-hour window. This presents an opportunity to improve urine tract infection diagnostic practices in healthcare settings., (© 2024. The Author(s).)

Purpose: Blood cultures (BCs) are key for pathogen detection in septic patients. We investigated the extent to which sampling was performed and what factors were associated with the absence of general or inadequate BC sampling., Methods: We conducted a retrospective cohort study of hospitalized patients with sepsis admitted to one of three EDs in 2018. Primary outcome was the extent of general BC collection of at least 1 set. Secondary outcome was the extent of adequate BC sampling, defined as ≥ 2 sets before antibiotic therapy (AT). Multivariable logistic regression analysis was performed to identify factors associated with deficits in both outcomes., Results: 1143 patients were analyzed. BCs were collected from 946 patients. Single BCs were taken from 520 patients, ≥ 2 sets from 426 patients. Overall, ≥ 2 BCs were taken from 349 patients before AT. BC sampling before AT occurred significantly more frequently when ≥ 2 BC sets were taken rather than a single one (81.9%, versus 68.4%, p < 0.001) and this also led to the highest pathogen detection rate in our cohort (65.6%). A body temperature of ≥ 38 °C was the a supporting factor for general and adequate BC collection in all three EDs. Retrospective analysis of 533 patients showed that the qSOFA score had no influence on general or adequate BC collection., Conclusion: Data on everyday clinical practice in the pre-analytical phase of microbiological diagnostics shows considerable deficits and indicates the need for more implementation of best practice. The variations identified in BC sampling between EDs should be further investigated., (© 2024. The Author(s).)

Viral load measurement of Respiratory syncytial virus (RSV) in acute bronchiolitis depends on specimen collection, viral load quantification, and transport media. The aim of this study was to investigate viral load in three-way-comparative analyses; nasal swab versus nasal wash, quantitative real-time polymerase chain reaction (RT-PCR) versus cell tissue culture, and various transport media. A prospective cohort study of infants aged < 12 months, admitted to the Soroka Medical Center, due to acute bronchiolitis, was conducted. Two nasal swabs and two nasal wash samples (in UTM and VCM) were collected from each infant upon admission and after 48 h. Samples were immediately stored at -80 °C and tested at Viroclinics DDL (Rotterdam, Netherlands). Quantitative RT-PCR and quantitative virus culture were performed using tissue culture infective dose (TCID50). Spearman's correlation coefficient test assessed the correlation between the different methods, viral load, and clinical severity score. One hundred samples were collected from 13 infants (mean age 5.7 ± 3.8 months, 46% males). Twelve patients were RSV-A positive, and one was RSV-B positive. A high correlation was found between transport media- UTM and VCM (0.92, P < 0.001) and between nasal swabs and nasal wash samples (0.62, P = 0.02). RSV signals were higher in nasal wash than in swabs. PCR signals were lower in the second collection compared to the first. No correlation was found between viral load and clinical severity.    Conclusion: RSV viral load is comparable across nasal wash, nasal swabs, and various transport media. However, it did not correlate with clinical severity, probably due to the limited sample size. Broader analyses are warranted. What is Known: • Viral load measurement in Respiratory Syncytial Virus (RSV) bronchiolitis depends on specimen collection, viral load quantification, and transport media. • The COVID-19 pandemic underscored the paramount significance of proper specimen collection, notably through nasal swabs. What is New: • RSV viral load was investigated in three-way-comparative analyses. • RSV viral load correlated well across PCR and tissue culture, nasal wash and swabs, and various transport media. RSV viral load did not correlate with clinical severity., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Laboratory study of natural populations of mosquitoes can play a key role in determining the underlying causes of variation in burdens of mosquito-borne disease. Aedes aegypti is the main vector of the viruses that cause dengue, chikungunya, Zika, and yellow fever, making it a high priority for laboratory study. Ae. aegypti eggs provide an ideal starting point for new laboratory colonies. Eggs can be collected using ovicups, which are small plastic cups lined with seed-germination paper and partially filled with leaf-infused H 2 O. Once collected, dry eggs will remain viable for months and can be safely transported long distances back to the laboratory as long as they are properly stored. This protocol provides step-by-step instructions for preparing for collecting, storing, and hatching Ae. aegypti eggs and has successfully yielded laboratory colonies from locations across both the native and invasive range of this species., (© 2024 Cold Spring Harbor Laboratory Press.)

Objectives: To evaluate the prevalence of bacterial presence in free-catch urine samples preceded by either a standardised prepped ("clean-catch") protocol versus unprepped (non-cleaned) voiding., Materials and Methods: The study was a single-centre prospective single-blinded randomised controlled trial. Urine samples were obtained from 100 client-owned dogs presenting for routine evaluation. Dogs were randomly assigned to either the prepped group (preputial or peri-vulvar area cleaned with sterile saline before collection) or the unprepped group (no preliminary cleansing) stratified by sex. Urinalysis and urine culture (blood and MacConkey agar) were performed on all samples. Significant bacterial presence on urine culture was defined as >10 4  colony forming units (CFU)/mL., Results: There were no statistically significant associations between prepped versus unprepped collection method or sex with a urinalysis positive for bacteriuria. However, on culture, significant bacterial growth was almost five times more likely to be associated with males relative to females (odds ratio 4.59, 95% confidence interval 1.61 to 13.10). The probability of finding a positive culture was not statistically associated with prep method (odds ratio 1.43, 95% confidence interval 0.50 to 4.08)., Clinical Significance: For the majority of dogs without clinical signs of urinary tract infection, free-catch urine collection does not result in significant bacteriuria found on analysis or culture. The presence of bacteria found in free-catch samples may be secondary to sample contamination or subclinical bacteriuria. Sample contamination or subclinical bacteriuria may be more prevalent in male dogs., (© 2024 British Small Animal Veterinary Association.)

Introduction: The purpose of the study was to analyze the effect of swabs on nasal mucosa., Methodology: Since May 2020, our department was responsible for screening coronavirus disease 2019 (COVID-19) among the employees of a company that continued its activity during the pandemic. The screening protocol consisted of two swabs per week. The samples were analyzed through objective endoscopic and subjective clinical evaluations with sino-nasal outcome test (SNOT Test) at three time points (T0, T1 - three months, T2 - six months)., Results: 23.76% of patients showed an increase in the SNOT score at T1, and the score decreased at T2. This could be due to the phenomenon of "adaptation" of the nasal mucosa. Endoscopic control showed that at T1, secretion, hyperemia, and edema are the most common signs. At T2, however, the crusts accounted for 52.94% of all damage. It is evident that at T1 the endoscopically detected signs of "acute" damage were more represented than at T2, while the signs of "chronic" damage increased as the number of swabs increased., Conclusions: We demonstrated that mucosal damage and perceived symptoms were absolutely acceptable compared to the diagnostic advantage obtained with serial screening., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2024 Giovanni Dell’Aversana Orabona, Vincenzo Abbate, Gianluca R De Fazio, Carlo Calvanese, Luigi Vaira, Paola Bonavolontà, Antonio Romano, Giovanni Improta, Pasquale Piombino, Luigi Califano.)

To accurately define the role of the gut microbiota in health and disease pathogenesis, the preservation of stool sample integrity, in terms of microbial community composition and metabolic function, is critical. This presents a challenge for any studies which rely on participants self-collecting and returning stool samples as this introduces variability and uncertainty of sample storage/handling. Here, we tested the performance of three stool sample collection/preservation buffers when storing human stool samples at different temperatures (room temperature [20 °C], 4 °C and - 80 °C) for up to three days. We compared and quantified differences in 16S rRNA sequencing composition and short-chain fatty acid profiles compared against immediately snap-frozen stool. We found that the choice of preservation buffer had the largest effect on the resulting microbial community and metabolomic profiles. Collectively analysis confirmed that PSP and RNAlater buffered samples most closely recapitulated the microbial diversity profile of the original (immediately - 80 °C frozen) sample and should be prioritised for human stool microbiome studies., (© 2024. The Author(s).)

The tear film is a highly dynamic biofluid capable of reflecting pathology-associated molecular changes, not only in the ocular surface but also in other tissues and organs. Molecular analysis of this biofluid offers a non-invasive way to diagnose or monitor diseases, assess medical treatment efficacy, and identify possible biomarkers. Due to the limited sample volume, collecting tear samples requires specific skills and appropriate tools to ensure high quality and maximum efficiency. Various tear sampling methodologies have been described in human studies. In this article, a comprehensive description of an optimized protocol is presented, specifically tailored for extracting tear-related protein information from experimental animal models, especially mice. This method includes the pharmacological stimulation of tear production in 2-month-old mice, followed by sample collection using Schirmer strips and the evaluation of the efficacy and efficiency of the protocol through standard procedures, SDS-PAGE, qPCR, and digital PCR (dPCR). This protocol can be easily adapted for the investigation of the tear protein signature in a variety of experimental paradigms. By establishing an affordable, standardized, and optimized tear sampling protocol for animal models, the aim was to bridge the gap between human and animal research, facilitating translational studies and accelerating advancements in the field of ocular and systemic disease research.