Colon or semicolon: gut sampling microdevices for omics insights.

Ingestible microdevices represent a breakthrough in non-invasive sampling of the human gastrointestinal (GI) tract. By capturing the native spatiotemporal microbiome and intricate biochemical gradients, these devices allow a non-invasive multi-omic access to the unperturbed host-microbiota crosstalk, immune/nutritional landscapes and gut-organ connections. We present the current progress of GI sampling microdevices towards personalized metabolism and fostering collaboration among clinicians, engineers, and data scientists.

Can pre-analytical procedures improve microbiological culture yield in patients with periprosthetic infections?

BACKGROUND: The detection of causative pathogens plays a crucial role in the diagnosis and targeted treatment of periprosthetic joint infections (PJI). While there have been improvements in analytic methods in the past, pre-analytical procedures have not yet been sufficiently investigated. The objective of this study was to compare the culture yield of four different pre-analytical procedures. METHODS: Patients with perioperative diagnosis of PJI were included in a single center cross-sectional study (2021-2022). Tissue samples (n = 20) of each patient were randomly and equally distributed to each of the four study arms. Tissue samples were either send to the laboratory without culture medium (group A) or were transported in thioglycolate medium immediately after sampling at three different temperatures (room temperature, 4 °C, 37° for 24 h; group B-D). Culture media were investigated for growth on days 1, 3, 7, 12, 14. All organisms, the number of positive samples and the time to positivity were recorded and compared between the study arms. Single positive cultures were considered as contamination. RESULTS: In total, 71 patients were included. The proportions of culture negative samples (10-15%) and polymicrobial infections (51-54%) were comparable between the four arms. Seven patients (10%) were culture-negative in group A, but showed growth in thioglycolate media (group B-D). Furthermore, 13% of patients showed growth in all groups, but additional organisms were cultured in thioglycolate. There was growth beyond day 7 of culturing only in thioglycolate, but not in group A. A storage temperature of 4 °C showed a longer time to positivity compared to the other groups (p < 0.001). CONCLUSIONS: Pre-analytical storage of tissue samples in thioglycolate broth did not improve the culture yield and did not detect additional cases of infection compared to the standard (pre-analytical storage in sterile containers). However, including a thioglycolate medium to the sampling algorithm reduced the rate of culture-negative infections and helped to identify additional organisms.

HPV self-sampling implementation strategies to engage under screened communities in cervical cancer screening: a scoping review to inform screening programs.

Introduction: Human papillomavirus (HPV) testing as a method of cervical cancer screening can be performed by healthcare providers or by patients through self-sampling directly in the community, removing several barriers experienced by under screened populations. The objective of this scoping review was to determine which HPV self-sampling implementation and engagement strategies have been used to engage under screened populations (i.e., Indigenous, newcomer, and rural and remote communities) in cervical cancer screening. Methods: A scoping review was conducted searching MEDLINE, CINAHL, EMBASE, Cochrane Library, and SocINDEX from inception to August 2023. The inclusion criteria were: (1) Indigenous, newcomer, and rural and remote communities; (2) countries identified as members of the Organization for Economic Co-operation and Development; and (3) intervention included HPV self-sampling. The review was registered prior to conducting the search (https://osf.io/zfvp9). Results: A total of 26 studies out of 2,741 studies met the inclusion criteria. In-person engagement with trusted community leaders was the most widely used and accepted recruitment and engagement strategy across all three populations. Six out of seven studies with Indigenous communities distributed HPV self-sampling kits to eligible participants in person in a clinical setting for collection on site or at home. Similarly, nine of the identified studies that engaged newcomers recruited participants in person through the community, where eligible participants were either given a kit (n = 7) or received one in the mail (n = 2). Lastly, of the 10 identified studies engaging rural and remote participants in HPV self-sampling, six recruited eligible participants in person at various community locations and four used electronic medical records or registries to identify and mail kits to participants. Discussion: HPV self-sampling through in person kit distribution and mail out of HPV self-sampling kits is an effective way to increase participation rates amongst under screened populations.

Progress, challenges, and future perspectives of robot-assisted natural orifice specimen extraction surgery for colorectal cancer: a review.

With the continuous advancements in precision medicine and the relentless pursuit of minimally invasive techniques, Natural Orifice Specimen Extraction Surgery (NOSES) has emerged. Compared to traditional surgical methods, NOSES better embodies the principles of minimally invasive surgery, making scar-free operations possible. In recent years, with the progress of science and technology, Robot-Assisted Laparoscopic Surgery has been widely applied in the treatment of colorectal cancer. Robotic surgical systems, with their clear surgical view and high operational precision, have shown significant advantages in the treatment process. To further improve the therapeutic outcomes for colorectal cancer patients, some scholars have attempted to combine robotic technology with NOSES. However, like traditional open surgery or laparoscopic surgery, the use of the robotic platform presents both advantages and limitations. Therefore, this study reviews the current research status, progress, and controversies regarding Robot-Assisted Laparoscopic Natural Orifice Specimen Extraction Surgery for colorectal cancer, aiming to provide clinicians with more options in the diagnosis and treatment of colorectal cancer.

Assessment of the Effective Sensitivity of SARS-CoV-2 Sample Pooling Based on a Large-Scale Screening Experience: Retrospective Analysis.

BACKGROUND: The development of new large-scale saliva pooling detection strategies can significantly enhance testing capacity and frequency for asymptomatic individuals, which is crucial for containing SARS-CoV-2. OBJECTIVE: This study aims to implement and scale-up a SARS-CoV-2 screening method using pooled saliva samples to control the virus in critical areas and assess its effectiveness in detecting asymptomatic infections. METHODS: Between August 2020 and February 2022, our laboratory received a total of 928,357 samples. Participants collected at least 1 mL of saliva using a self-sampling kit and registered their samples via a smartphone app. All samples were directly processed using AutoMate 2550 for preanalytical steps and then transferred to Microlab STAR, managed with the HAMILTON Pooling software for pooling. The standard pool preset size was 20 samples but was adjusted to 5 when the prevalence exceeded 2% in any group. Real-time polymerase chain reaction (RT-PCR) was conducted using the Allplex SARS-CoV-2 Assay until July 2021, followed by the Allplex SARS-CoV-2 FluA/FluB/RSV assay for the remainder of the study period. RESULTS: Of the 928,357 samples received, 887,926 (95.64%) were fully processed into 56,126 pools. Of these pools, 4863 tested positive, detecting 5720 asymptomatic infections. This allowed for a comprehensive analysis of pooling's impact on RT-PCR sensitivity and false-negative rate (FNR), including data on positive samples per pool (PPP). We defined Ctref as the minimum cycle threshold (Ct) of each data set from a sample or pool and compared these Ctref results from pooled samples with those of the individual tests (ΔCtP). We then examined their deviation from the expected offset due to dilution [ΔΔCtP = ΔCtP - log2]. In this work, the ΔCtP and ΔΔCtP were 2.23 versus 3.33 and -0.89 versus 0.23, respectively, comparing global results with results for pools with 1 positive sample per pool. Therefore, depending on the number of genes used in the test and the size of the pool, we can evaluate the FNR and effective sensitivity (1 - FNR) of the test configuration. In our scenario, with a maximum of 20 samples per pool and 3 target genes, statistical observations indicated an effective sensitivity exceeding 99%. From an economic perspective, the focus is on pooling efficiency, measured by the effective number of persons that can be tested with 1 test, referred to as persons per test (PPT). In this study, the global PPT was 8.66, reflecting savings of over 20 million euros (US $22 million) based on our reagent prices. CONCLUSIONS: Our results demonstrate that, as expected, pooling reduces the sensitivity of RT-PCR. However, with the appropriate pool size and the use of multiple target genes, effective sensitivity can remain above 99%. Saliva pooling may be a valuable tool for screening and surveillance in asymptomatic individuals and can aid in controlling SARS-CoV-2 transmission. Further studies are needed to assess the effectiveness of these strategies for SARS-CoV-2 and their application to other microorganisms or biomarkers detected by PCR.

Invitation strategy of vaginal HPV self-sampling to improve participation in cervical cancer screening: a systematic review and meta-analysis of randomized trials.

BACKGROUND: Human papillomavirus (HPV) self-sampling is recognized as a feasible option for enhancing screening for cervical cancer, particularly among hard-to-reach women. The magnitude of the effectiveness of screening participation under different invitation strategies was reported. This review seeks to compare the effectiveness of invitation strategies in increasing screening participation of HPV self-sampling across diverse study settings. METHODS: A systematic literature search was conducted in Embase, MEDLINE, and PubMed in April 2023. Articles were included if (1) their target participants were aged between 25 and 70 years; (2) participants in the intervention arm were randomized to receive HPV self-sampling devices through various invitation strategies; (3) participants in the control arm who either received invitations for cervical cancer screening other than HPV self-sampling or opportunistic screening as usual care; (4) studies that provided sufficient data on screening participation in HPV self-sampling as outcome measured. The study design of the included articles was limited to randomized controlled trials. RESULTS: A total of 15 articles were included in this review. Invitation strategies of disseminating HPV self-sampling devices included opt-out and opt-in. Meta-analysis revealed screening participation in the self-sampling group was significantly greater than control arm (OR 3.43, 95% CI 1.59-7.38), irrespective of the invitation strategy employed. Among invitation strategies, opt-out appeared to be more effective on increasing screening participation, compared to control and opt-in strategy (opt-out vs. control OR 3.91, 95% CI 1.82-8.42; opt-in vs. control OR 1.34, 95% CI 0.28-6.39). CONCLUSIONS: Opt-out strategy is more successful at improving screening participation compared to opt-in and routine invitation to cervical screening. It is therefore a promising way to improve participation in cervical cancer screening. The findings of this review provide important inputs to optimize strategies for inviting women to participate in vaginal HPV self-sampling across the study setting, thus improving participation in cervical cancer screening.

Validation of Saliva as the Clinical Specimen Type for a University-Wide COVID-19 Surveillance Program.

At the beginning of the COVID-19 pandemic, the Georgia Institute of Technology made the decision to keep the university doors open for on-campus attendance. To manage COVID-19 infection rates, internal resources were applied to develop and implement a mass asymptomatic surveillance program. The objective was to identify infections early for proper follow-on verification testing, contact tracing, and quarantine/isolation as needed. Program success depended on frequent and voluntary sample collection from over 40,000 students, faculty, and staff personnel. At that time, the nasopharyngeal (NP) swab, not saliva, was the main accepted sample type for COVID-19 testing. However, due to collection discomfort and the inability to be self-collected, the NP swab was not feasible for voluntary and frequent self-collection. Therefore, saliva was selected as the clinical sample type and validated. A saliva collection kit and a sample processing and analysis workflow were developed. The results of a clinical sample-type comparison study between co-collected and matched NP swabs and saliva samples showed 96.7% positive agreement and 100% negative agreement. During the Fall 2020 and Spring 2021 semesters, 319,988 samples were collected and tested. The program resulted in maintaining a low overall mean positivity rate of 0.78% and 0.54% for the Fall 2020 and Spring 2021 semesters, respectively. For this high-throughput asymptomatic COVID-19 screening application, saliva was an exceptionally good sample type.

Evaluation of testing face-mask filter samples with LAMP shows high rates of detection in pulmonary TB.

Detection of Mycobacterium tuberculosis (MTB) in bioaerosols derived from patients with active pulmonary TB is a potential alternative diagnostic method for patients with presumed TB who cannot expectorate sputum.To assess the efficacy of a bioaerosol particle collection method to capture MTB and diagnose TB.A mask-like filter holder (3D mask) with a water-soluble gelatine filter (GF) and one containing a water-insoluble polypropylene filter (PPF) were prepared. Eligible patients wore the 3D mask with GF or PPF within 3 days of starting anti-TB drugs. The GF and PPF filters were collected after 2 and 8 h. DNA was extracted from the filter samples and tested using loop-mediated isothermal amplification (LAMP).Filter samples were collected from 57 and 20 patients with and without active pulmonary TB, respectively. The GF and PPF sensitivity was 76.2% and 83.3%, respectively. The specificity of both methods was 100%. Of the 57 patients diagnosed with non-expectorated sputum samples, including suction phlegm, gastric lavage, and bronchial lavage fluid, 55.6% and 50.0% were positive by GF and PPF, respectively.We present a 3D mask filter sampling method for exhaled bioaerosol particles that can be used in clinical practice to diagnose patients with presumed TB..

Understanding the preferences of young women in self-sampling interventions for sexually transmitted infection diagnosis: a discrete choice experimental protocol.

INTRODUCTION: Sexually transmitted infections (STIs) are a significant public health concern globally, particularly affecting young women. Early diagnosis and treatment are essential to reducing or stopping the continuous spread of infections and the development of associated complications. Syndromic management, which is commonly used for STIs, presents several barriers, particularly for young women. This protocol is for a study that aims to understand young women's preferences for a self-sampling intervention for STI diagnosis by using a discrete choice experiment (DCE). The DCE will be conducted among young women residing in underserved urban communities in eThekwini Metropolitan Municipality in KwaZulu-Natal, South Africa. METHODS AND ANALYSIS: The following attributes of a self-sampling intervention were identified through a Nominal Group Technique: accessibility, education, confidentiality, self-sampling method, youth-friendliness and cost. A pilot study involving 20 participants was conducted to refine the DCE questionnaire. A total of 196 young women from underserved communities will be recruited. The participants will be sampled from communities, stratified by settlement type and socioeconomic status. Data will be analysed using the multinomial logit model and mixed logit model to assess preferences and heterogeneity. ETHICS AND DISSEMINATION: The study was approved by the Faculty of Health Sciences Research Ethics Committee of the University of Pretoria. The study findings have the potential to inform policies for STI treatment and management to align healthcare services with user preferences. This can improve STI healthcare access for young women in underserved communities. Ethical approval was obtained, and results will be disseminated through peer-reviewed journals and health conferences.

Making bloodwork work: the impact of sample collection, processing, and storage on plasma glutathione measurement, and implications for translation.

Psychiatry has traditionally focused on the study of neurons and neurotransmitter physiology in the pathophysiology and treatment of psychiatric disorders. A growing literature highlights REDOX imbalance (a state in which demand for antioxidants surpasses their bioavailability) as a common pathophysiology for a diverse array of brain conditions (e.g., trichotillomania, schizophrenia, autism, Parkinson's disease). REDOX imbalance is typically measured via plasma glutathione, as glutathione is critical to the adaptive antioxidant response in the brain. Accordingly, glutathione, its precursors, and/or metabolites serve as biomarkers of disease risk, therapeutic targets, and measures of treatment response. However, as with any emerging field, there are currently several different methods for collection, processing, storage, and calculation of summary measures of plasma glutathione metabolism, within and between preclinical and clinical research. The lack of evidence-based best-practice methodology hampers reproducibility (preclinical or clinical), and translation (between preclinical and clinical work). To address this methodological need, here we used a repeated measures within-subject design to investigate how sample preparation (type of anticoagulant used during blood collection, deproteinization status, and storage temperature) affects plasma glutathione levels. Accordingly, we collected whole blood from mice (N = 13), and then, using a commercially available kit, quantified glutathione in plasma stored in four different ways. Presuming that these preparation conditions and post-processing calculations are unimportant, we would expect to see no difference in glutathione levels and summary measures from the same sample. However, we found each of these variables to significantly alter quantified glutathione levels. Accordingly, we propose a vital, gold-standard methodology for both sample collection, processing, and storage of plasma used for glutathione quantification and for summary calculations of glutathione that can be used preclinically and clinically, thus yielding more streamlined translation.

Human papillomavirus self-sampling and urine-sampling tests and the management and short-term outcomes of cervical intraepithelial neoplasia: A prospective observational study.

AIM: The importance of human papillomavirus (HPV) co-testing using physician-, self-, and urine-collected samples to predict cervical intraepithelial neoplasia (CIN) grade 1-2 prognoses has not been previously reported. Therefore, this study aimed to investigate outcomes of patients with CIN 1-2 who simultaneously underwent physician-, self-, and urine-collection sampling tests. METHODS: This study was conducted in Japan between October 2019 and November 2022 and examined the proportion of cases with CIN 1-2 progressions, the percentage of cases with persistent CIN 1-2, and the outcome differences according to the results of physician-, self-, and urine-sampling tests. RESULTS: There were 105 and 59 CIN 1 and 2 cases, respectively, with progression or persistence in 27 (29.3%) and 21 (50.0%) cases, respectively. The median follow-up was 20 and 12 months, respectively. Progression and persistence of CIN 1 were significantly associated with HPV-positive physician- and self-collected samples. No significant difference was observed between cases with CIN 2 who had HPV-positive and HPV-negative results using any sampling method. CONCLUSIONS: Physician- and self-testing for HPV are crucial for predicting disease progression risk in CIN 1 cases. Future research with an extended observation period and consideration of the progression risks is warranted.

Protocol for a clinically annotated biorepository of samples from Australian immune-compromised patients to investigate the host-microbiome interaction.

INTRODUCTION: The human gut microbiota has the potential to modulate the outcomes of several human diseases. This effect is likely to be mediated through interaction with the host immune system. This protocol details the establishment of a biorepository of clinically annotated samples, which we will use to explore correlations between the gut microbiota and the immune system of immune-compromised patients. We aim to identify microbiome-related risk factors for adverse outcomes. METHODS AND ANALYSES: This is a protocol for the development of a biorepository of clinically annotated samples collected prospectively across three centres in Melbourne, Australia. Participants will be recruited across the following clinical streams: (1) acute leukaemia and allogeneic stem cell transplant; (2) end-stage liver disease and liver transplant; (3) patients receiving any cancer immunotherapies (eg, chimeric antigen receptor therapy); (4) deceased organ donors and (5) healthy adult controls. Participants will be asked to provide paired peripheral blood and microbiota samples (stool and saliva) at either (1) single time point for healthy controls and deceased organ donors or (2) longitudinally over multiple prespecified or event-driven time points for the remaining cohorts. Sampling of fluid from bronchoalveolar lavage and colonoscopy or biopsy of tissues undertaken during routine care will also be performed. ETHICS AND DISSEMINATION: Ethical approval has been obtained from the relevant local ethics committee (The Royal Melbourne Hospital Human Research Ethics Committee). The results of this study will be disseminated by various scientific platforms including social media, international presentations and publication in peer-reviewed journals. TRIAL REGISTRATION NUMBER: ACTRN12623001105639. Date registered 20 October 2023.

Benchmarking sample pooling for epigenomics of natural populations.

DNA methylation (DNAm) is a mechanism for rapid acclimation to environmental conditions. In natural systems, small effect sizes relative to noise necessitates large sampling efforts to detect differences. Large numbers of individually sequenced libraries are costly. Pooling DNA prior to library preparation may be an efficient way to reduce costs and increase sample size, yet there are to date no recommendations in ecological epigenetics research. We test whether pooled and individual libraries yield comparable DNAm signals in a natural system exposed to different pollution levels by generating whole-epigenome data from two invasive molluscs (Corbicula fluminea, Dreissena polymorpha) collected from polluted and unpolluted localities (Italy). DNA of the same individuals were used for pooled and individual epigenomic libraries and sequenced with equivalent resources per individual. We found that pooling effectively captures similar genome-wide and global methylation signals as individual libraries, highlighting that pooled libraries are representative of the global population signal. However, pooled libraries yielded orders of magnitude more data than individual libraries, which was a consequence of higher coverage. We would therefore recommend aiming for a high initial coverage of individual libraries (15×) in future studies. Consequently, we detected many more differentially methylated regions (DMRs) with the pooled libraries and a significantly lower statistical power for regions from individual libraries. Computationally pooled data from the individual libraries produced fewer DMRs and the overlap with wet-lab pooled DMRs was relatively low. We discuss possible causes for discrepancies, list benefits and drawbacks of pooling, and provide recommendations for future epigenomic studies.

Sample collecting methods for bacterial community structure analysis of scalp hair: non-invasive swabbing versus intrusive hair shaft cutting.

Human skin samples for microbiome analysis are traditionally collected using a non-invasive swabbing method. Here, we compared the differences in bacterial community structures on scalp hair and scalps with samples collected using non-invasive swabbing and cutting/removal of scalp hair in 12 individuals. Hair-related samples, such as hair shafts and hair swabs, had significantly higher alpha diversity than scalp swab samples, whereas there were no significant differences between hair shafts and hair swabs. The relative abundances of the three major phyla and five major operational taxonomic units were not significantly different between the hair shaft and hair swab samples. The principal coordinate analysis plots based on weighted UniFrac distances were grouped into two clusters: samples from hair-related areas and scalp swabs, and there were significant differences only between samples from hair-related areas and scalp swabs. In addition, a weighted UniFrac analysis revealed that the sampling site-based category was a statistical category but not a hair sampling method-based category. These results suggest that scalp hair bacteria collected using non-invasive swab sampling were comparable to those collected cutting/removal of scalp hair.

Sexual behavior stigma and HIV/STI biospecimen self-collection among cisgender gay, bisexual, and other sexually minoritized men in the United States.

INTRODUCTION: Disparities in HIV and other sexually transmitted infections (STIs) persist among cisgender sexually minoritized men in the United States, driven in part by sexual behavior stigma, which is a barrier to clinic-based HIV/STI testing. HIV/STI biospecimen self-collection (HSBS) is a novel testing approach that mitigates stigma by allowing for some testing-related procedures to be conducted by oneself in one's home or any private location rather than a facility that requires interpersonal interactions and exposure to other members of the public. HSBS has demonstrated acceptability, feasibility, and effectiveness in testing uptake, but the extent to which stigma persists in HSBS and the quantification of stigma's role in HSBS is limited. METHODS: From 2019-2020, a nationwide sample of sexually minoritized men completed an online biobehavioral survey. Those who agreed to be recontacted (N = 4147) were invited to participate in HSBS; consented participants received self-collection kits that were laboratory-tested if completed. Sexual behavior stigma and HSBS associations were assessed with logistic regression. RESULTS: Mean age of participants was 35 years, 58% (2421/4147) were non-Hispanic white, 82% (3391/4147) were gay-identifying, 47% (1967/4147) had at least a college degree, and 56% (2342/4147) earned ≥ $40,000 annually; 27% (1112/4147) expressed HSBS interest, and 67% (689/1034) completed HSBS. HSBS interest and completion were less common among non-Hispanic Black sexually minoritized men and sexually minoritized men of lower socioeconomic status. Stigma from family and friends was significantly, negatively associated with HSBS interest (aOR = 0.72, 95% CI = 0.56, 0.93). Among those who had not tested for HIV/STIs in the past year, anticipated healthcare stigma was marginally, negatively associated with HSBS completion (aOR = 0.40, 95% CI = 0.15, 1.07). Among those who had never previously tested for HIV/STIs, anticipated healthcare stigma was significantly, negatively associated with HSBS interest (aOR = 0.32, 95% CI = 0.14, 0.72). CONCLUSIONS: Sexual behavior stigma persists as an HIV/STI testing barrier, even in the case of HSBS, limiting its utilization. Increasing HSBS among sexually minoritized men in the US necessitates stigma mitigation efforts that directly address equity in implementation.

A two-stage location model covering COVID-19 sampling, transport and DNA diagnosis: design of a national scheme for infection control.

During the COVID-19 pandemic, a system was established in China that required testing of all residents for COVID-19. It consisted of sampling stations, laboratories capable of carrying out DNA investigations and vehicles carrying out immediate transfer of all samples from the former to the latter. Using Beilin District, Xi'an City, Shaanxi Province, China as example, we designed a genetic algorithm based on a two-stage location coverage model for the location of the sampling stations with regard to existing residencies as well as the transfer between the sampling stations and the laboratories. The aim was to estimate the minimum transportation costs between these units. In the first stage, the model considered demands for testing in residential areas, with the objective of minimizing the costs related to travel between residencies and sampling stations. In the second stage, this approach was extended to cover the location of the laboratories doing the DNAinvestigation, with the aim of minimizing the transportation costs between them and the sampling stations as well as the estimating the number of laboratories needed. Solutions were based on sampling stations and laboratories existing in 2022, with the results visualized by geographic information systems (GIS). The results show that the genetic algorithm designed in this paper had a better solution speed than the Gurobi algorithm. The convergence was better and the larger the network size, the more efficient the genetic algorithm solution time.

Challenges for pathologists in implementing clinical microbiome diagnostic testing.

Recent research has established that the microbiome plays potential roles in the pathogenesis of numerous chronic diseases, including carcinomas. This discovery has led to significant interest in clinical microbiome testing among physicians, translational investigators, and the lay public. As novel, inexpensive methodologies to interrogate the microbiota become available, research labs and commercial vendors have offered microbial assays. However, these tests still have not infiltrated the clinical laboratory space. Here, we provide an overview of the challenges of implementing microbiome testing in clinical pathology. We discuss challenges associated with preanalytical and analytic sample handling and collection that can influence results, choosing the appropriate testing methodology for the clinical context, establishing reference ranges, interpreting the data generated by testing and its value in making patient care decisions, regulation, and cost considerations of testing. Additionally, we suggest potential solutions for these problems to expedite the establishment of microbiome testing in the clinical laboratory.

How storage post sampling influences the stability of sebum when used for mass spectrometry metabolomics analysis?

Sebum is a biofluid excreted by sebaceous glands in the skin. In recent years sebum has been shown to contain endogenous metabolites diagnostic of disease, with remarkable results for Parkinson's Disease. Given that sebum sampling is facile and non-invasive, its potential for use in clinical biochemistry diagnostic assays should be explored including the parameters for standard operating procedures around collection, transport, and storage. To this aim we have here investigated the reproducibility of mass spectrometry data from sebum in relation to both storage temperature and length of storage. Sebum samples were collected from volunteers and stored for up to four weeks at a range of temperatures: ambient (circa 17 °C), -20 °C and -80 °C. Established extraction protocols were employed and samples were analysed by two chromatographic mass spectrometry techniques and data investigated using PCA, PLS-DA and ANOVA. We cannot discriminate samples as a function of storage temperature or time stored in unsupervised analysis using data acquired via TD-GC-MS and LC-IM-MS, although the sampling of volatiles was susceptible to batch effects. This study indicates that the requirements for storage and transport of sebum samples that may be used in clinical assays are less stringent than for liquid samples and indicate that sebum is suitable for remote and at home sampling prior to analysis.

HPV self-collection for cervical cancer screening among survivors of sexual trauma: a qualitative study.

Intimate partner violence affects 20-30% of women in the United States. Disparities in routine cervical cancer surveillance have been demonstrated in certain populations, including victims of intimate partner violence (IPV). This study examined and assessed the acceptability of high-risk HPV (hrHPV) self-collection among individuals who have experienced IPV. We conducted an observational study using qualitative data collection and analysis. We interviewed individuals with a history of IPV and who currently reside in Oregon. This study identified key themes describing knowledge and attitudes towards cervical cancer screening for individuals who have experienced IPV. They include: guideline knowledge, prior office-based cervical cancer screening experience, barriers to cervical cancer screening, at-home hrHPV self-collection experience, and testing confidence. Participants experienced fewer barriers and expressed increased comfort and control with hrHPV self-collection process. Individuals with a history of IPV have lower rates of cervical cancer screening adherence and higher rates of cervical dysplasia and cancer than other populations. The patient-centered approach of hrHPV self-collection for cervical cancer screening can reduce barriers related to the pelvic exam and empower patients to reduce their risks of developing cervical cancer by enabling greater control of the testing process.

Comparison of RT-PCR cycle threshold values between individual and pooled SARS-CoV-2 infected nasopharyngeal swab specimens.

The molecular reverse transcription-polymerase chain reaction (RT-PCR) testing of respiratory tract swabs has become mandatory to confirm the diagnosis of coronavirus disease 2019 (COVID-19). However, RT-PCR tests are expensive, require standardized equipment, and relatively long testing times, and the sample pooling method has been introduced to solve this issue. The aim of this study was to compare the cycle threshold (Ct) values of the individual sample and pooled sample methods to assess how accurate the pooling method was. Repeat RT-PCR examinations were initially performed to confirm the Ct values for each sample before running the pooled test procedure. Sample extraction and amplification were performed in both assays to detect ORF1ab, N, and E genes with a cut-off point value of Ct <38. Overall, there was no difference in Ct values between individual sample and pooled sample groups at all concentrations (p=0.259) and for all pooled sizes. Only pooled size of five could detect the Ct value in the pooled samples for all concentration samples, including low-concentration sample (Ct values 36 to 38). This study highlighted that pooled RT-PCR testing strategy did not reduce the quality of individually measured RT-PCR Ct values. A pool size of five could provide a practical technique to expand the screening capacity of RT-PCR.