Authentic Pathology Specimen Reception: A Valuable Resource for Developing Biomedical Science Student Competencies and Employability.

Background/Introduction: The pathology specimen reception is fundamental to the services provided by Biomedical Science laboratories worldwide. To ensure patient safety and that samples are of adequate quality to send for analysis, prospective Biomedical Scientists should have a robust knowledge of the processes involved and the acceptance criteria of the pathology specimen reception. This knowledge has been highlighted by employers as a current gap in Biomedical Science graduates and therefore needs to be addressed within higher education settings. To do this, this study aimed to 1) design a practical session to simulate the key processes of the pathology specimen reception and 2) to understand Biomedical Science students' opinions on these activities and the development of transferable skills required for post-graduate employment. Methods: The practical session was designed based on industrial requirements and academic knowledge of student skill sets to ensure suitability. Qualitative information regarding participant demographics and career interests was acquired through open-answer or multiple-choice questions. Quantitative student feedback was acquired via questionnaires utilising a 5-point Likert scale (n = 77). Results: The scenario-based practical session provided students with a positive learning experience with 98.7% of participants enjoying the session, with 87.0% stating they learned a lot by completing the session. It was also identified that participants preferred this style of learning to that of conventional higher education teaching modalities with 97.4% stating they would prefer simulated employment focussed scenarios embedded into the curriculum more often. The majority of participants also thought this session was helpful for the development of their key transferrable skills including teamworking, communication, and confidence. When stratified based on demographic data, there was minimal difference between cohorts and in the majority of cases, those participants from non-traditional university entry backgrounds had a more positive experience and better transferable skill development following the completion of this style of learning experience. Conclusion: This study highlights simulation-based learning as a tool to develop core Biomedical Science knowledge, build student graduate capital, and ensure the preparedness of students for post-graduation employment.

Assessment of thermal and temporal stability of SARS-CoV-2 samples using real-time qRT-PCR.

BACKGROUND: As per the guidelines of the Indian Council of Medical Research, nasopharyngeal and oropharyngeal swabs in viral transport medium (VTM) are to be stored at 4 °C for less than 5 days and for more than 5 days at -70 °C. Samples are not transported or stored as per prescribed conditions because of the limitations, resulting in an apprehensive diagnosis. The aim of the study was to test the stability of the SARS-CoV-2 sample stored in VTM at different temperatures. METHODS: In this study, the stability of 21 positive and 9 negative samples for SARS-CoV-2 was evaluated in commercial VTM at different temperatures (-80 °C, -20 °C, 4 °C, and 25 to 30 °C). Stability was checked for up to 50 days in the above storage conditions at different intervals. PathoDetect™ and Hi-PCR® kits were used for the detection of the four genes of SARS-CoV-2. The Cycle Threshold (Ct) value for determining the positivity of samples for PathoDetect™ was < 40 and for Hi-PCR® was < 38. RESULTS: The SARS-CoV-2 confirmatory genes (RdRp and E genes) and the internal housekeeping gene remained detectable even on the 50th day of the study. The Ct of the RdRp and E genes were found to increase with storage duration, but all positive samples remained positive till the end of the study, or the Ct value remained below the cut-off level. The negative samples gave consistent results until the end of the study. When the differences in Ct values were compared between the days in a set of experiments, they were not significantly different except in a few samples. CONCLUSION: The SARS-CoV-2 genetic materials in commercial VTM were stable at room temperature to -80 °C for 50 days.

Livmorhalsprøvetaking i primærhelsetjenesten.

BACKGROUND: In Norway, approximately 360 000 cervical screening samples were taken in 2020, of which 11 000 were registered as inadequate. We therefore wished to investigate doctors' knowledge of cervical sample-taking in the primary health service. MATERIAL AND METHOD: An anonymous survey on cervical sample-taking was sent by email to around 4 700 members of the Norwegian College of General Practice in September 2021. RESULTS: Of the 1 039 doctors who responded to the survey, 820 (79 %) reported that they always indicate the reason for taking the sample in the requisition form, and 898 (86 %) reported that they avoid taking a sample during menstruation. Only one in three doctors (343) correctly indicated the location of the squamocolumnar junction in postmenopausal women. In response to a question aimed at users of the ThinPrep method, which is particularly sensitive to sampling errors, 426 out of 697 (61 %) answered that they either avoid using a lubricant or use a water-based lubricant, while only 35 % of the doctors responded that they stop taking the sample if bleeding occurs. INTERPRETATION: The results show that although many doctors have satisfactory knowledge, a continuous focus on cervical sample-taking is essential. Correct sampling and knowledge of anatomical factors in postmenopausal women may be significant for reducing the number of inadequate samples.

Com Ciência e Com Respeito: episódio 15

O que são Biobancos? Para que servem? Como são formados? E principalmente: como garantir os direitos dos participantes de pesquisa que têm seus materiais biológicos guardados nesses lugares? Descubra aqui, ouvindo este episódio.

Factors influencing platelet isolation: a prospective multicenter study from Western China.

Tumor-educated platelets (TEPs) have been widely reported to have promising application potential; nonetheless, platelet isolation from peripheral blood is an important but neglected step in TEPs research for platelet-based liquid biopsy. In this article, we discussed some common influence factors for platelet isolation. To investigate the factors involved in platelet isolation, a prospective multicenter study was conducted on healthy Han Chinese adults (18 to 79 years of age). A total of 208 individuals were included in the final statistical analysis out of the 226 healthy volunteers who were prospectively enrolled from four hospitals. The primary study metric was the platelet recovery rate (PRR). The similar pattern was observed in the four hospitals, The PRR at room temperature (23°C±2°C) was slightly higher than the PRR at cold temperature (4°C±2°C). Moreover, the PRR gradually decreased as the storage time increased. The PRR for samples within 2 hours of storage is significantly higher than for samples beyond 2 hours (p < .05). Additionally, PRR was also affected by the equipment used in different centers. This study confirmed several factors that influence platelet isolation. In our study, we indicated that platelet isolation should be performed within two hours of peripheral blood draw and held at room temperature until isolation, and that centrifuge models should be fixed during the extraction process, which will further improve the research progress of platelet-based liquid biopsy in cancer.

What is the context? Globally, cancer is one of the leading cause of premature death. Early screening is important for cancer diagnosis and treatment and can even significantly lower cancer mortalityGlobally, cancer is one of the leading cause of premature death. Early screening is important for cancer diagnosis and treatment and can even significantly lower cancer mortalityFor the liquid biopsy, isolation is an important step. Early studies have explored the influencing factors of exosome, circulating tumor cells (CTCs), and other components extraction in liquid biopsy.Despite platelet also being an excellent source of liquid biopsy, few studies have explored the factors that influence platelet isolation.Considering the importance of platelet isolation in tumor-based platelet liquid biopsy, our aim is to optimize platelet isolation conditions as much as possible to obtain a high platelet recovery rate.What is new? In this study, we conducted a prospective multicenter study ofhealthy adults from four centers, combining whole blood with platelet-richplasma to investigate factors influencing platelet recovery rate (PRR) during platelet isolation.In our study, we indicated that platelet isolation should be performed within two hours at room temperature, and that centrifuge models should be fixed during the extraction process, which will further improve the research progress of platelet-based liquid biopsy in cancer.What is the impact? In future platelet-related studies, we should fix the sample storage temperature, storage time and centrifuge model in the process of platelet extraction, so as to reduce the variables affecting platelet extraction as much as possible and ensure the stable recovery rate of platelet extraction.

Directrices de laboratorio para la detección y el diagnóstico de la infección por el virus de la viruela del mono / Laboratory Guidelines for the Detection and Diagnosis of Monkeypox Virus Infection

Este documento está basado en la guía provisional de la Organización Mundial de la Salud sobre las pruebas de laboratorio para el virus de la viruela del mono, 23 de mayo de 2022, y tiene por objeto proporcionar orientación a los Laboratorios Nacionales de Referencia sobre la detección del virus de la viruela del mono

This document is based on World Health Organization interim guidance on Laboratory testing for monkeypox virus, 23 May 2022, and is intended to provide guidance to National Reference Laboratories on monkeypox virus laboratory detection

Blood culture contamination in the departments of paediatrics and child health at two tertiary training hospitals in central South Africa.

BACKGROUND: Bloodstream infections are an important cause of mortality in children. Blood cultures (BCs) remain the primary means of identifying organisms and their antibiotic susceptibility profiles. A shortcoming of BCs is that up to 56% of positive cultures will represent contaminants. Poor adherence to standard practices applicable to BC sampling could explain an unacceptable contamination rate. OBJECTIVES: To determine: (i) the BC contamination rate in the departments of paediatrics and child health at two tertiary hospitals in central South Africa; and (ii) BC sampling practices among paediatric clinicians. METHODS: The author determined the prevalence of BC contamination by analysis of laboratory data for the period 1 May - 27 August 2019, and assessed possible factors contributing to BC contamination by surveying paediatric medical staff with a self-administered BC practices questionnaire. RESULTS: Of the 244 BCs reviewed, 25.4% were positive. The most commonly isolated pathogens were coagulase-negative staphylococci (CoNS) (33.3%), Escherichia coli (22.2%), Enterococcus faecium (16.7%) and Acinetobacter baumannii (11.1%). In total, 15.2% of the BCs yielded contaminants and 2.9% had polymicrobial growth. The most common contaminant was CoNS. Approximately 68% of clinicians were not aware of BC sampling guidelines, and even among those who were aware of the guidelines, non-compliance was reported. CONCLUSIONS: The BC contamination rate was higher than internationally accepted rates. Educating clinicians on specific BC sampling guidelines is strongly recommended to decrease the high rate of contamination observed in this study.

Merits and pitfalls of normal saline rehydrated air-dried cervical smears over conventional wet.fixed PAP smears: A comparative study.

BACKGROUND: Cervical Papanicolaou (PAP) smear is the simplest, minimal invasive, and excellent screening method to reduce the female morbidity and mortality due to cervical carcinoma. Immediate alcohol fixation of the cervical smears is required to preserve nuclear details, delay in alcohol fixation leads to air drying artifacts. Rehydrating of the air-dried cervical pap smear with normal saline can help to overcome these artifacts and also have its own advantages. AIMS: This study was design to evaluate the effects, merits and pitfalls of normal saline Rehydrated Air-Dried Cervical PAP Smears (RADPS) compared with the Conventional Papanicolaou Smear (C-PAPS). SETTINGS AND DESIGN: Comparative study. METHODS AND MATERIAL: Prospectively paired cervical smears of 100 women, who presented to the outpatient department of gynecology of our institute, were prepared. Alcohol fixed smears were labelled as conventional Papanicolaou smear (C-PAPS) and air-dried smears labelled as rehydrated air-dried PAP smears (RADPS). Eight cytomorphological parameters were considered for comparison and analyzed. STATISTICAL ANALYSIS USED: Chisquare (χ2)/Fisher exact test. RESULTS: Clear background with red blood cells (RBC) lysis was noted in 93% of RADPS and 54% of C-PAPS. Cytolysis was observed more in C-PAPS (18%) than in RADPS (08%). Air-drying artifacts observed in 30% of C-PAPS and 08% of RADPS. Cytoplasmic staining (92% of RADPS and 85% of C-PAPS) was superior in RADPS. Cell border, nuclear chromatin, and border were also better appreciated on RADPS as compared to C-PAPS. Statistically significant difference was observed with 3 parameters, i.e., air-drying artifacts, RBC background, and distinct cell borders. CONCLUSION: Rehydration of air-dried smears can be adopted in regular practice, as an alternative or coupled with conventional wet fixation method to overcome the commonly faced problems of air-drying artifacts, especially in rural screening programs.

Evaluation of Different Cleaning Strategies for Removal of Contaminating DNA Molecules.

Decontamination strategies and their efficiencies are crucial when performing routine forensic analysis, and many factors influence the choice of agent to use. In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. Cell-free DNA or blood was deposited on three surfaces (plastic, metal, and wood) and decontaminated with various treatments. The quantities of recovered DNA, obtained by swabbing the surfaces after cleaning using the different strategies, was analyzed by real-time PCR. Large differences in the DNA removal efficiencies were observed between different cleaning strategies, as well as between different surfaces. The most efficient cleaning strategies for cell-free DNA were the different sodium hypochlorite solutions and Trigene®, for which a maximum of 0.3% DNA was recovered on all three surfaces. For blood, a maximum of 0.8% of the deposited DNA was recovered after using Virkon® for decontamination. The recoveries after using these cleaning strategies correspond to DNA from only a few cells, out of 60 ng of cell-free DNA or thousands of deposited blood cells.

COVID-19 Serology Control Panel Using the Dried-Tube Specimen Method.

The dried-tube specimen (DTS) procedure was used to develop the COVID-19 serology control panel (CSCP). The DTS offers the benefit of shipping materials without a cold chain, allowing for greater access without deterioration of material integrity. Samples in the panel were sourced from COVID-19 convalescent persons from March to May 2020. The immunoglobulin subtypes (total Ig, IgM, and IgG) and their respective reactivity to severe acute respiratory syndrome coronavirus 2 nucleocapsid, spike, and receptor-binding domain antigens of the samples were delineated and compared with the WHO International Standard to elucidate the exact binding antibody units of each CSCP sample and ensure the CSCP provides adequate reactivity for different types of serological test platforms. We distribute the CSCP as a kit with five coded tubes to laboratories around the world to be used to compare test kits for external quality assurance, for harmonizing laboratory testing, and for use as training materials for laboratory workers.

Assessing the quality of RNA isolated from human breast tissue after ambient room temperature exposure.

High quality human tissue is essential for molecular research, but pre-analytical conditions encountered during tissue collection could degrade tissue RNA. We evaluated how prolonged exposure of non-diseased breast tissue to ambient room temperature (22±1°C) impacted RNA quality. Breast tissue received between 70 to 190 minutes after excision was immediately flash frozen (FF) or embedded in Optimal Cutting Temperature (OCT) compound upon receipt (T0). Additional breast tissue pieces were further exposed to increments of 60 (T1 = T0+60 mins), 120 (T2 = T0+120 mins) and 180 (T3 = T0+180 mins) minutes of ambient room temperature before processing into FF and OCT. Total exposure, T3 (T0+180 mins) ranged from 250 minutes to 370 minutes. All samples (FF and OCT) were stored at -80°C before RNA isolation. The RNA quality assessment based on RNA Integrity Number (RIN) showed RINs for both FF and OCT samples were within the generally acceptable range (mean 7.88±0.90 to 8.52±0.66). No significant difference was observed when RIN at T0 was compared to RIN at T1, T2 and T3 (FF samples, p = 0.43, 0.56, 0.44; OCT samples, p = 0.25, 0.82, 1.0), or when RIN was compared between T1, T2 and T3. RNA quality assessed by quantitative real-time PCR (qRT-PCR) analysis of beta-actin (ACTB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclophilin A (CYPA), and porphobilinogen deaminase (PBGD) transcripts showed threshold values (Ct) that indicate abundant and intact target nucleic acid in all samples (mean ranging from 14.1 to 25.3). The study shows that higher RIN values were obtained for non-diseased breast tissue up to 190 minutes after resection and prior to stabilization. Further experimental exposure up to 180 minutes had no significant effect on RIN values. This study strengthens the rationale for assessing RIN and specific gene transcript levels as an objective method for determining how suitable RNA will be for a specific research purpose ("fit-for purpose").

Sequence locally, think globally: The Darwin Tree of Life Project.

The goals of the Earth Biogenome Project-to sequence the genomes of all eukaryotic life on earth-are as daunting as they are ambitious. The Darwin Tree of Life Project was founded to demonstrate the credibility of these goals and to deliver at-scale genome sequences of unprecedented quality for a biogeographic region: the archipelago of islands that constitute Britain and Ireland. The Darwin Tree of Life Project is a collaboration between biodiversity organizations (museums, botanical gardens, and biodiversity institutes) and genomics institutes. Together, we have built a workflow that collects specimens from the field, robustly identifies them, performs sequencing, generates high-quality, curated assemblies, and releases these openly for the global community to use to build future science and conservation efforts.

Optimizing liquefaction and decontamination of sputum for DNA extraction from Mycobacterium tuberculosis.

Whole genome sequencing (WGS) can investigate the entire Mycobacterium tuberculosis (Mtb) genome but currently requires large amounts of mycobacterial DNA, necessitating culture. Culture-free Mtb WGS could revolutionize the clinical use of WGS but is hampered by the high viscosity, low mycobacterial load, and high contamination with bacterial and human DNA in sputum samples. To improve the sputum liquefaction and decontamination step prior to DNA extraction, we assessed the efficiency of Myco-TB, MycoPrep, and Sputolysin with/without TiKa-Kic in liquefying and decontaminating sputum and aimed to evaluate the effect of these approaches on mycobacterial viability, and Mtb DNA quality and quantity. Experiments using spiked sputum samples showed that Myco-TB and BD MycoPrep with standard (15 min) or increased (30 min) incubation time, but not reduced (7,5 min) incubation time performed well in liquefying and decontaminating sputum. No difference in DNA quality or quantity, contamination, or the amount of human DNA present was observed. In comparison, Sputolysin with/without TiKa-Kic was less effective for liquefaction and decontamination of sputum. PCR amplification of the human GAPDH gene after sputum treatment, showed the presence of human DNA in all samples, regardless of sputum treatment. Focused efforts are needed to deplete contaminating DNA for culture-free Mtb WGS.

Defining the Healthy Infant Metabolome: Liquid Chromatography Tandem-Mass Spectrometry Analysis of Dried Blood Spot Extracts from the Prospective Research on Early Determinants of Illness and Children's Health Trajectories Birth Cohort Study.

Newborn screening using dried plasma spots offers preanalytical advantages over conventional cards for plasma-associated targets of interest. Herein we present dried plasma spot-based methods for measuring metabolites using a 250+ compound liquid chromatography tandem mass spectrometry library. Quality assurance reduced this library to 134, and from these, 30 compounds determined the normal newborn reference ranges.

Feasibility and acceptability of frequent vaginal self-sampling at home by Rwandan women at high risk of urogenital tract infections.

OBJECTIVES: To establish temporal links between vaginal microbiota (VMB) data and incident clinical events, frequent longitudinal vaginal sampling is required. Self-collection of swabs at the participant's home may be useful to avoid overburdening research clinics and participants. One-off vaginal self-sampling for STI or cervical cancer screening programmes has been shown to be feasible and acceptable to women in multiple studies, including in sub-Saharan Africa, but the feasibility and acceptability of frequent longitudinal vaginal sampling in the context of VMB sequencing studies is unknown. METHODS: Twelve participants of a randomised clinical trial in Kigali, Rwanda, self-collected vaginal swabs three times a week for a month. We studied feasibility by comparing DNA concentrations, proportions of samples with >1000 16S rRNA amplicon sequencing reads and VMB composition outcomes of self-collected swabs with clinician-collected swabs. We evaluated the acceptability of self-collection using structured face-to-face interviews and a focus group discussion. RESULTS: The participants collected vaginal swabs at 131 different time points. One woman stopped self-sampling after one try due to a social harm. All self-sampled swabs generated >1000 rRNA amplicon sequencing reads, and the DNA concentration of self-sampled swabs and clinician-sampled swabs did not differ significantly (Kruskal-Wallis p=0.484). Self-sampled and clinician-sampled swabs generated similar VMB composition data. Participants reported feeling very comfortable during self-sampling (11/12; 91.7%) and that self-sampling had become easier over time (12/12; 100%). They mentioned reduced travel time and travel costs as advantages of self-sampling at home. CONCLUSIONS: Frequent longitudinal vaginal sampling at home is feasible and acceptable to participants, even in the context of a low-resource setting, as long as adequate counselling is provided. TRIAL REGISTRATION NUMBER: NCT02459665.

The feasibility of field collected pig oronasal secretions as specimens for the virologic surveillance of Japanese encephalitis virus.

Virologic surveillance of Japanese encephalitis virus (JEV) relies on collecting pig blood specimens and adult mosquitoes in the past. Viral RNAs extracted from pig blood specimens suffer from low detecting positivity by reverse transcription PCR (RT-PCR). The oronasal transmission of the virus has been demonstrated in experimentally infected pigs. This observation suggested oronasal specimens could be useful source in the virus surveillance. However, the role of this unusual route of transmission remains unproven in the operational pig farm. In this study, we explore the feasibility of using pig oronasal secretions collected by chewing ropes to improve the positivity of detection in commercial pig farms. The multiplex genotype-specific RT-PCR was used in this study to determine and compare the positivity of detecting JEV viral RNAs in pig's oronasal secretions and blood specimens, and the primary mosquito vector. Oronasal specimens had the overall positive rate of 6.0% (95% CI 1.3%-16.6%) (3/50) to 10.0% (95% CI 2.1%-26.5%) (3/30) for JEV during transmission period despite the negative results of all blood-derived specimens (n = 2442). Interestingly, pig oronasal secretions and female Culex tritaeniorhynchus mosquito samples collected from the same pig farm showed similar viral RNA positive rates, 10.0% (95% CI 2.1%-26.5%) (3/30) and 8.9% (95% CI 2.5%-21.2%) (4/45), respectively (p> 0.05). Pig oronasal secretion-based surveillance revealed the seasonality of viral activity and identified closely related genotype I virus derived from the mosquito isolates. This finding indicates oronasal secretion-based RT-PCR assay can be a non-invasive, alternative method of implementing JEV surveillance in the epidemic area prior to the circulation of virus-positive mosquitoes.

Underutilization and Quality Gaps in Blood Culture Processing in Public Hospitals of Peru.

Correct processing of blood cultures may impact individual patient management, antibiotic stewardship, and scaling up of antimicrobial resistance surveillance. To assess the quality of blood culture processing, we conducted four assessments at 16 public hospitals across different regions of Peru. We assessed the following standardized quality indicators: 1) positivity and contamination rates, 2) compliance with recommended number of bottles/sets and volume of blood sampled, 3) blood culture utilization, and 4) possible barriers for compliance with recommendations. Suboptimal performance was found, with a median contamination rate of 4.2% (range 0-15.1%), with only one third of the participating hospitals meeting the target value of < 3%; and a median positivity rate of 4.9% (range 1-8.1%), with only 6 out of the 15 surveilled hospitals meeting the target of 6-12%. None of the assessed hospitals met both targets. The median frequency of solitary blood cultures was 71.9% and only 8.9% (N = 59) of the surveyed adult bottles met the target blood volume of 8 - 12 mL, whereas 90.5% (N = 602) were underfilled. A high frequency of missed opportunities for ordering blood cultures was found (69.9%, 221/316) among patients with clinical indications for blood culture sampling. This multicenter study demonstrates important shortcomings in the quality of blood culture processing in public hospitals of Peru. It provides a national benchmark of blood culture utilization and quality indicators that can be used to monitor future quality improvement studies and diagnostic stewardship policies.