Short Turnaround Time Research Articles

Evaluation of a multiplex real-time PCR targeting the β-tubulin gene for the detection and differentiation of Sporothrix schenckii and Sporothrix brasiliensis.

Sporothrix sp. is a thermally dimorphic genus of fungi known to cause subacute or chronic subcutaneous lesions in humans and animals and is the cause of increasing public health concern due to spread of feline-associated cases. Here, we adapted and evaluated a recently described real-time PCR assay targeting the β-tubulin gene to rapidly detect and differentiate two related species, S. schenckii and S. brasiliensis. The assay was tested with 55 S. brasiliensis, 19 S. schenckii, and 85 isolates from other clinically relevant fungi, and showed 100% concordance with reference identification methods. The assay showed high analytical sensitivity with a limit of detection of 1 pg of DNA per microliter of sample for both targets. The assay was further evaluated with 11 fresh and 17 formalin-fixed, paraffin-embedded (FFPE) tissues. This multiplex real-time PCR assay successfully detected the DNA from both S. brasiliensis and S. schenckii isolates as well as S. schenckii from fresh and FFPE tissues. Our results demonstrate this assay performs well and could be a helpful molecular tool to support rapid species identification in cultures and primary specimens.IMPORTANCEHaving available molecular tools to identify and differentiate closely related species will allow clinical, veterinarians, and public health labs to provide diagnostic results with accuracy and short turnaround time for the routine and outbreak response activities.

A Descriptive Study: Evaluation of Delayed Laboratory Testing in Emergency Room

Precision, accuracy, and short turnaround time (TAT) are important to improve the quality and effectiveness of laboratory services in the Emergency Room (ER). Several studies reported an average of 60% the ratio of anticoagulant to sample is not appropriate, lysis, and clotted samples occurred in the pre-analytical part. This part consisted of the request/registration of laboratory tests, patient preparation, specimen collection, and transportation to the central laboratory. The aim of this research is to evaluate the cause of the long TAT for laboratory research so as to obtain problem solving based on the target. This observational study was conducted in 2021 at the ER laboratory outlet. Observations were made started from the workload carried out by the laboratory technician, sample registration, and data collection from the Laboratory Information System (LIS). The study obtained 14.709 samples from the LIS at the Clinical Pathology Department, Cipto Mangunkusumo Hospital. The highest sample rejection rate was from the ER laboratory outlet due to specimen lysis (2.79%). The average time required for re-collecting specimens was around 2-2.5 hours. This rejection was below the minimum quality standards based on the International Federation of Clinical Chemistry (IFCC). Other problems include the limited number of medical laboratory experts compared to the workload also inefficient Computerized Physician Order Entry (CPOE) registration methods. The main problem of delayed laboratory testing in the emergency department is the pre-analytical part including sample registration and rejection specimens. That rejection mostly comes from lysis specimens, which caused invalid laboratory result.

B-023 Workflow evaluation of the new Siemens Atellica CI Analyzer

Abstract Background The Atellica® CI Analyzer, Model 1900 is an integrated clinical chemistry and immunoassay analyzer that has the same user interface, general workflow, and planned test menu to that of the larger Atellica® Solution. Atellica CI Analyzer also shares the same reagents and consumables as the Atellica Solution. The purpose of this study was to evaluate workflow performance of the Atellica CI Analyzer in a routine-like clinical laboratory setting. Methods The study was conducted at four international laboratory facilities over a four-month period. Basic throughput of the Atellica CI Analyzer was evaluated at each site by testing quality control (QC) and remnant anonymized patient samples using an 8:2 mixture of chemistry (ion selective electrolytes [IMT], clinical chemistry analytes) and immunochemistry assays. Additionally, the impact of interrupting routine testing for STAT high-sensitivity cardiac troponin samples was also evaluated. Daily, weekly, and monthly maintenance activities were observed, and data collected through direct observations, time and motion studies, and system run logs. Results The Atellica CI Analyzer aspirated patient samples in as little as two minutes (mins) with the time to first result for the mixed assay worklist ranging from 1 to 12 mins from the time of first barcode read. Across the four sites, the time to last result for the mixed assay worklist (average n=495 test results per site) ranged from 52 to 65 mins. The average turn around time (TAT) for high-sensitivity troponin was 9 mins from barcode read. Daily maintenance and QC activities for the Atellica CI Analyzer are comprised of both automated and manual activities. The average daily maintenance hands-on time was 3.6 min, ranging from 1.6 to 6.4 mins across the four sites. Daily QC preparation required <5 mins of hands-on time. The total average hands-on time to complete weekly maintenance for the Atellica CI Analyzer was 7.5 min. Conclusions The Atellica CI Analyzer demonstrated consistent system performance across all four study sites. Implementation of the Atellica CI Analyzer has the potential to increase laboratory efficiency given the minimal hands-on time required for daily and weekly maintenance activities and short TATs.

Clinical evaluation of a multiplex PCR-based test for joint infection: a prospective diagnostic accuracy study of forty-nine patients

PurposeThe purpose of this study was to evaluate the diagnostic accuracy (sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV)) of the PCR-based BioFire® Joint Infection Panel (BJI Panel) against microbiological culture growth for patients suspected of having a native or prosthetic joint infection.MethodsSynovial fluid and tissue biopsies were prospectively collected from patients from June 2022 to June 2023. The results of the BJI Panel were compared with those of culture growth.Results51 samples were included. Including all pathogens, the sensitivity was 69%, the specificity 89%, the PPV 73% and the NPV 86%. Including only pathogens in the BJI Panel, the sensitivity was 100%, the specificity 90%, the PPV 73% and the NPV 100%.ConclusionThe BJI Panel has a high accuracy for detecting the pathogens in its panel, but the absence of important common pathogens from the panel reduces its sensitivity and NPV. With a short turnaround time and precise pathogen detection, the BJI Panel has the potential to add value as a complementary diagnostic method.

A-359 Clinical Performance Evaluation of the Polymerase Chain Reaction (PCR)-Based cobas CT/NG/MG Test for Use on the cobas liat System in a Clinical Laboratory Setting and Point-of-Care (POC) Location

Abstract Background Screening for Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Mycoplasma genitalium (MG) can be achieved rapidly (in approximately 20 minutes) with the cobas® CT/NG/MG test (assay not cleared by US FDA. Submission currently under review and subject to change per health authority feedback). This automated, qualitative, real-time PCR-based nucleic acid amplification test (NAAT) is for use on the cobas® liat® system. This study evaluated the test’s clinical performance using urogenital samples from symptomatic and asymptomatic patients. Methods This non-interventional, non-observational study used prospective clinician-collected and self-collected specimens (urine, and vaginal swabs, all in cobas® PCR Media) from symptomatic/asymptomatic patients ≥14 years old from 13 POC sites across the US. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of cobas liat CT/NG/MG were calculated with respect to patient infected status (PIS), as determined using results from three FDA-approved NAATs and one laboratory-developed test. Due to insufficient positive NG samples during the trial period, further testing used archived samples. Results The median (range) age of the study population (N=4,800) was 35.0 (15.0-81.0) years; 40.4% (n=1,941) were symptomatic and 51.9% (n=2,489) were assigned female at birth. The cobas CT/NG/MG nucleic acid test demonstrated good clinical performance (Table 1). Across all specimen types, specificity was >97% for each analyte. Sensitivity was ≥95%, except in female urine (CT 87.0%, NG 93.1%, MG 78.9%). Regardless of specimen type, PPV and NPV were ≥95% for CT and NG; PPV for MG was highest in male urine (92.7%) and NPV was >97.5% across analytes. Conclusions In a clinical setting, the cobas CT/NG/MG nucleic acid test showed good clinical performance for the detection of CT, NG, and MG in urogenital samples, in addition to providing a short turn-around time and centralized testing lab quality at the POC for both self- and clinician-collected samples.

Simultaneous CNV-seq and WES: An effective strategy for molecular diagnosis of unexplained fetal structural anomalies

BackgroundFetal structural anomalies are detected by ultrasound in approximately 3 % of pregnancies. Numerous genetic diagnostic strategies have been widely applied to identify the genetic causes of prenatal abnormalities. We aimed to assess the value of simultaneous copy number variation sequencing (CNV-seq) and whole exome sequencing (WES) in diagnosing fetuses with structural anomalies. MethodsFetuses with structural anomalies detected by ultrasound were included for eligibility. After genetic counseling, WES and CNV-seq were performed on DNA samples of fetuses and their parents. All detected variants were evaluated for pathogenicity according to ACMG criteria, with the final diagnosis was determined based on ultrasound results and relevant family history. ResultsThe diagnostic rate of 174 fetuses with prenatal ultrasound abnormalities was 26.44 %, higher than that achieved through either CNV or WES analysis alone. Furthermore, the highest diagnostic rate was observed in fetuses with multiple system anomalies, accounting for 50 % of the total diagnostic yield, followed by skeletal system anomalies at 45.45 %. Three cases with multiple system abnormalities were found to have a dual diagnosis of pathogenic CNVs and SNV variants, representing 1.72 % of the total cohort. 38 pregnant women in their third trimester of pregnancy (27 weeks+) participated in this study, and 23.68 % received a confirmed genetic diagnosis. Finally, 31 women (67.39 %) voluntarily terminated their pregnancy following the testing and extensive genetic counseling. ConclusionsOur study demonstrated that the simultaneous CNV-seq and WES analyses are beneficial for the molecular diagnosis of underlying unexplained structural anomalies in fetuses. This strategy is more efficient in elucidating prenatal abnormalities with compound problems, such as dual diagnoses. Furthermore, the simultaneous strategy has a shorter turnaround time and is particularly suitable for families with structural anomalies found in the third trimester of pregnancy.

Validation of short culture method for rapid bacterial identification of blood cultures via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Development of rapid bacterial identification from blood cultures has been an area of intense study in diagnostic microbiology. Shortened turnaround time coupled with antimicrobial stewardship interventions have been shown to improve patient outcomes and decrease healthcare-associated costs. We report the validation of a short incubation method for Gram-positive and Gram-negative bacterial identification utilizing MALDI-TOF MS without additional instrumentation, processing or cost compared with current practice. Prospective, observational, single-centre study in a quaternary care academic hospital encompassing 376 blood cultures subjected to bacterial identification after short incubation periods of 3-4 and 6-8 h. There was 97.5% species-level identification agreement with tests undertaken after 3-4 h incubation with 83.6% isolates identified, and 99.7% species-level identification agreement after 6-8 h incubation with 96.7% isolates identified. The short incubation method provides a rapid MALDI-TOF MS bacterial identification method, reducing turnaround time by 10-18 h compared with standard practice without additional cost, processing or instrumentation.

Enterprise supply chain network optimization algorithm based on blockchain-distributed technology under the background of digital economy

Demand forecasting is essential for streamlining supply chain operations in the digital economy and exceeding customer expectations. On the other hand, traditional forecasting techniques cannot frequently present real-time data and respond to dynamic changes in the supply chain network, leading to less-than-ideal decision-making and higher costs. This research aims to create a technique for optimizing the supply chain network based on blockchain-distributed technology (SCN-BT) to overcome these drawbacks and fully utilize the potential of the digital economy. The suggested framework uses the hybridized LSTM network and Grey Wolf Optimization (GWO) algorithm to examine demand forecasting in the supply chain network for inventory planning. The SCN-BT framework develops a safe and productive, enabling precise and flexible demand by combining blockchain with optimization techniques. A thorough case study utilized information collected from an enterprise supply chain that operates in the digital economy to show the efficiency of the suggested framework. Compared to conventional approaches, the results show considerable gains in demand forecasting precision, responsiveness of the supply chain, and cost-effectiveness. In the context of the digital economy, demand sensing and prediction enable firms to react to changes swiftly, shorten turnaround times, optimize inventory levels, and improve overall supply chain performance. The results highlight how blockchain technology has the potential to enhance collaboration, trust, and transparency inside intricate supply chain networks working in the digital economy. The experimental results show the proposed to achieve prediction rate of demand prediction rate of 128.93, demand forecasting accuracy ratio of 92.18%, optimum efficiency of 94.25%, RMSE rate of 1841.25, MAE rate of 260.74, and sMAPE rate of 0.1002 compared to other methods.

Clinical evaluation of a highly multiplexed CRISPR-based diagnostic assay for diagnosing lower respiratory tract infection: a prospective cohort study

Objective Accurate and rapid identification of causative pathogens is essential to guide the clinical management of lower respiratory tract infections (LRTIs). Here we conducted a single-centre prospective study in 284 patients suspected of lower respiratory tract infections to evaluate the utility of a nucleic acid test based on highly multiplexed polymerase chain reaction (PCR) and CRISPR-Cas12a. Methods We determined the analytical and diagnostic performance of the CRISPR assay using a combination of reference standards, including conventional microbiological tests (CMTs), metagenomic Next-Generation Sequencing (mNGS), and clinical adjudication by a panel of experts on infectious diseases and microbiology. Results The CRISPR assay showed a higher detection rate (63.0%) than conventional microbiological tests (38.4%) and was lower than metagenomic Next-Generation Sequencing (72.9%). In detecting polymicrobial infections, the positivity rate of the CRISPR assay (19.4%) was higher than conventional microbiological tests (3.5%) and lower than metagenomic Next-Generation Sequencing (28.9%). The overall diagnostic sensitivity of the CRISPR assay (67.8%) was higher than conventional microbiological tests (41.8%), and lower than metagenomic Next-Generation Sequencing (93.2%). Conclusions Considering the low cost, ease of operation, short turnaround time, and broad range of pathogens detected in a single test, the CRISPR assay has the potential to be implemented as a screening tool for the aetiological diagnosis of lower respiratory tract infections patients, especially in cases where atypical bacteria or coinfections are suspected.

Prosigna Assay for Treatment Decisions in Early Breast Cancer: A Decision Impact Study.

Introduction: Therapeutic decisions in early breast cancer are based on clinico-pathological features which are subject to intra- and inter-observer variability. This single-center decision impact study aimed to evaluate the effects of the Prosigna assay on physicians' adjuvant treatment choices. Methods: Between 09/2017 and 02/2018, formalin-fixed tumor samples from 52 newly diagnosed, postmenopausal, hormone receptor-positive, HER2-negative breast cancer (T1-T2; pN0-N1a) patients were analyzed. Pre-test clinical judgements and Prosigna test results were compared. Results: The mean age was 59 (42-77). Invasive ductal carcinoma (79.2%), grade 2 (52.8%) and T1c-N0 tumors (43.4%) were represented. There was 40.4% discordance between the pre- and post-test risk of recurrences. No significant change was observed in the clinical intermediate risk category, while there was a net reclassification of low-risk patients into a high Prosigna recurrence risk group. In addition, clinically determined intrinsic subtypes were 34.6% discordant with the Prosigna results, which is largely driven by the reclassification of the luminal A tumors into the Prosigna-assessed luminal B group. Before the Prosigna test, endocrine treatment was the primary choice in 20 patients (39.2%), and chemotherapy was recommended to 31 patients (60.8%). Overall, the Prosigna assay led to a change in treatment choice for one patient. Conclusions: Although conventional risk assessment methods are relatively inexpensive with shorter turnaround times, their accuracy and value for risk reduction are suboptimal. According to our results, the Prosigna assay was found to be a relevant tool for the clinical decision making process. Long-term follow-up of these patients will elucidate the potential benefits of using multigene molecular tests as biomarkers for treatment.

Microbiological Evaluation of Two Mexican Artisanal Cheeses: Analysis of Foodborne Pathogenic Bacteria in Cotija Cheese and Bola de Ocosingo Cheese by qPCR.

Cotija and Bola de Ocosingo are artisanal ripened cheeses produced in Mexico. Both are made with raw bovine milk from free-grazing cows and with no starter cultures. Unlike culture-based techniques, molecular methods for pathogen detection in food allow a shorter turnaround time, higher detection specificity, and represent a lower microbiological risk for the analyst. In the present investigation, we analyzed 111 cheese samples (95 Cotija and 16 Bola de Ocosingo) by qPCR (TaqMan®) after an enrichment-culture step specific to each foodborne bacterium. The results showed that 100% of the samples were free of DNA from Listeria monocytogenes, Brucella spp., Escherichia coli enterotoxigenic (ETEC), and O157:H7; 9% amplified Salmonella spp. DNA; and 11.7%, Staphylococcus aureus DNA. However, the threshold cycle (Ct) values of the amplified targets ranged between 23 and 30, indicating DNA from non-viable microorganisms. Plate counts supported this assumption. In conclusion, 100% of the cheeses analyzed were safe to consume, and the enrichment step before DNA extraction proved essential to discern between viable and non-viable microorganisms. Hygienic milking, milk handling, cheese manufacturing, and ripening are crucial to achieve an adequate microbiological quality of cheeses made with raw milk.

Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling.

Imagine if we could simultaneously predict spatial protein expression in tissues from their routine Hematoxylin and Eosin (H&E) stained images, and create tissue images given protein expression profiles thus enabling virtual simulations of how protein expression alterations impact histology in complex diseases like cancer. Such an approach could lead to more informed diagnostic and therapeutic decisions for precision medicine at lower costs and shorter turnaround times, more detailed insights into underlying disease pathology as well as improvement in predictive and generative performance. In this study, we investigate the intricate correlation between protein expressions obtained from Hyperion mass cytometry and histopathological microstructures in conventional H&E stained glioblastoma (GBM) samples, unveiling morphological patterns and cellular-level spatial alterations associated with protein expression changes. To model these complex relationships, we propose a novel generative-predictive framework called Ouroboros for producing H&E images from protein expressions and simultaneously predicting protein expressions from H&E images. Our comprehensive sample-independent validation over 9920 tissue spots from 4 GBM samples encompassing visual image analysis, quantitative analysis, subspace alignment and perturbation experiments shows that the proposed generative-predictive approach offers significant improvements in predicting protein expression from images in comparison to baseline methods as well as accurate generation of virtual GBM sample images. This proof of concept study can contribute to advancing our understanding of histological responses to protein expression perturbations and lays the foundations for further developments in this area. Implementation and associated data for the proposed approach are available at the URL: https://github.com/Srijay/Ouroboros.

Efavirenz: New Hope in Cancer Therapy.

Despite extensiveresearch directedat preventive and treatment strategies, breast cancer remains the leading cause of cancer-related mortality among women. This necessitates the development of a new medication aimed at increasing patient survival and quality of life. A new drug's development from the ground up can cost billions of dollars and take up to ten or more years. Because much of the required safety and pharmacokinetic data are already available from earlier trials, repurposing medications usually results in lower costs and shorter turnaround times. Many antiretroviral medications target biological pathways and enzymes associated with cancer, which becomes an ideal option for repurposing as anticancer medications. Efavirenz is an antiretroviral medication that targets molecular pathways implicated in the growth of breast cancer, such as LINE-1 (long interspersed nuclear elements-1) suppression, hence lowering the proliferation of breast cancer cells and exhibiting anti-cancer properties. Additionally, it suppresses the fatty acid synthase gene and other important genes related to fat metabolism, impairing mitochondrial activity and making cancer cells deprived of energy. Efavirenz also inhibits cancer-initiating stem cells, promotes differentiation, and prevents recurrence. Additionally, efavirenz promotes oxidative damage bythe formation of superoxide in cancer cells. In addition to its anti-cancer properties, efavirenz has the advantage of being a well-established and relatively inexpensive medication with a favorable safety profile. If proven effective, efavirenz could offer a cost-effective therapeutic option, which is an intriguing direction that warrants further investigation.

Challenges of liquid panel in genomic profiling of esophageal squamous cell carcinoma (ESCC): Insights from an analysis of over 1000 cases.

86 Background: Genomic analysis of ctDNA from cancer patients can allow identification of actionable alterations of tumor without an invasive biopsy. ctDNA analysis has been reported to be superior for global summary of tumor heterogeneity and a short turnaround time compared to tissue analysis,however, there are potential issues including the detection sensitivity, threshold to determine TMB-H, and clonal hematopoiesis of indeterminate potential (CHIP). In order to elucidate the impact of ctDNA analysis on personalized cancer treatment, we decided to examine the genetic landscape and clinical outcomes of ESCC cohort registered in the C-CAT database. Methods: We retrospectively analyzed data from 1059 cases of ESCC registered in the C-CAT from June 2019 to February 2024. Clinical characteristics, TMB status, pathological gene variants, and time to treatment failure (TTF) of first-line treatment were examined. Results: The panels applied to eligible patients consisted of 925 tumor tissue panels (87.3%) and 134 liquid panels (12.7%). Pathological gene mutations were detected in 924 cases (99.8%) in tissue panels and 133 cases (99.2%) in liquid panels. The top 10 detected genes were TP53 (93.4%), CDKN2A (57.8%), CDKN2B (45.5%), CCND1 (43.9%), FGF19 (41.0%), PIK3CA (29.0%), NFE2L2 (28.3%), BCL6 (16.5%), NOTCH1 (13.5%), and KMT2D (12.2%). The detection rate for these genes excluding NOTCH1 and KMT2D were significantly higher in tissue panels than in liquid panels (P≤0.01). The median TMB was 5.00 Muts/Mb for both. In first-line treatment, the TTF for immune checkpoint inhibitors (ICIs) and chemotherapy was significantly longer in TMB-H (≧10 Muts/Mb) compared to TMB-L (3.1M vs. 1.9M, P<0.01) in patients evaluated by tissue panels, but it was not proven in patients evaluated by liquid panels (P=0.38). Furthermore, the results suggest that patients with CDKN2A, CCND1, and FGF19 variants benefit more by adding ICIs to chemotherapy than patients without these variants and while the opposite was true for BCL6 and NOTCH1 and KMT2D. Conclusions: In this ESCC cohort, detection rates in the liquid panels were generally lower than in the tissue panels, suggesting that sufficient ctDNA could not be obtained in many cases. The appropriate patient selection for the liquid panels and the timing of blood collection should be discussed. Furthermore, the ideal threshold for determining TMB-H in the liquid panels needs to be further investigated.

Clinical Utility of Optical Genome Mapping for Improved Cytogenomic Analysis of Gliomas.

A glioma is a solid brain tumor which originates in the brain or brain stem area. The diagnosis of gliomas based on standard-of-care (SOC) techniques includes karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), for detecting the pathogenic variants and chromosomal abnormalities. But these techniques do not reveal the complete picture of genetic complexity, thus requiring an alternative technology for better characterization of these tumors. The present study aimed to evaluate the clinical performance and feasibility of using optical genome mapping (OGM) for chromosomal characterization of gliomas. Herein, we evaluated 10 cases of gliomas that were previously characterized by CMA. OGM analysis showed concordance with the results of CMA in identifying the characterized Structural Variants (SVs) in these cases. More notably, it also revealed additional clinically relevant aberrations, demonstrating a higher resolution and sensitivity. These clinically relevant SVs included cryptic translocation, and SVs which are beyond the detection capabilities of CMA. Our analysis highlights the unique capability of OGM to detect all classes of SVs within a single assay, thereby unveiling clinically significant data with a shorter turnaround time. Adopting this diagnostic tool as a standard of care for solid tumors like gliomas shows potential for improving therapeutic management, potentially leading to more personalized and timely interventions for patients.

Specific and Sensitive Visual Proviral DNA Detection of Major Pathogenic Avian Leukosis Virus Subgroups Using CRISPR-Associated Nuclease Cas13a.

Avian leukosis viruses (ALVs) include a group of avian retroviruses primarily associated with neoplastic diseases in poultry, commonly referred to as avian leukosis. Belonging to different subgroups based on their envelope properties, ALV subgroups A, B, and J (ALV-A, ALV-B, and ALV-J) are the most widespread in poultry populations. Early identification and removal of virus-shedding birds from infected flocks are essential for the ALVs' eradication. Therefore, the development of rapid, accurate, simple-to-use, and cost effective on-site diagnostic methods for the detection of ALV subgroups is very important. Cas13a, an RNA-guided RNA endonuclease that cleaves target single-stranded RNA, also exhibits non-specific endonuclease activity on any bystander RNA in close proximity. The distinct trans-cleavage activity of Cas13 has been exploited in the molecular diagnosis of multiple pathogens including several viruses. Here, we describe the development and application of a highly sensitive Cas13a-based molecular test for the specific detection of proviral DNA of ALV-A, B, and J subgroups. Prokaryotically expressed LwaCas13a, purified through ion exchange and size-exclusion chromatography, was combined with recombinase polymerase amplification (RPA) and T7 transcription to establish the SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) molecular detection system for the detection of proviral DNA of ALV-A/B/J subgroups. This novel method that needs less sample input with a short turnaround time is based on isothermal detection at 37 °C with a color-based lateral flow readout. The detection limit of the assay for ALV-A/B/J subgroups was 50 copies with no cross reactivity with ALV-C/D/E subgroups and other avian oncogenic viruses such as reticuloendotheliosis virus (REV) and Marek's disease virus (MDV). The development and evaluation of a highly sensitive and specific visual method of detection of ALV-A/B/J nucleic acids using CRISPR-Cas13a described here will help in ALV detection in eradication programs.

The Next Frontier in Tuberculosis Investigation: Automated Whole Genome Sequencing for Mycobacterium tuberculosis Analysis.

A fully automated bacteria whole genome sequencing (WGS) assay was evaluated to characterize Mycobacterium tuberculosis (MTB) and non-tuberculosis Mycobacterium (NTM) clinical isolates. The results generated were highly reproducible, with 100% concordance in species and sub-lineage classification and 92% concordance between antimicrobial resistance (AMR) genotypic and phenotypic profiles. Using extracted deoxyribonucleic acid (DNA) from MTB clinical isolates as starting material, these findings demonstrate that a fully automated WGS assay, with a short turnaround time of 24.5 hours, provides timely and valuable insights into MTB outbreak investigation while providing reliable genotypic AMR profiling consistent with traditional antimicrobial susceptibility tests (AST). This study establishes a favorable proposition for the adoption of end-to-end fully automated WGS solutions for decentralized MTB diagnostics, thereby aiding in World Health Organization's (WHO) vision of tuberculosis eradication.

Utilization of international normalized ratio-derived formula to predict plasma rivaroxaban level-Validation study and real-world experience.

Specific assays of plasma rivaroxaban level are not always readily available with short turnaround time, which hamper the management of urgent clinical situations. In this study, we aimed to build a predictive formula of plasma rivaroxaban levels from international normalized ratio (INR) value and validated in real world clinical situations. Ninety-four patients who were taking rivaroxaban participated in the study. Patients were randomized into testing cohort and validation cohorts. The prediction formula was built from the testing cohort and then validated in validation cohort. The predictive performance was further validated on real-world clinical requests. The root mean square error (RMSE) of the predictive formula for the testing and validation cohorts were 61.81 and 69.32 ng/mL, respectively. The sensitivity and specificity for the formula to predict the threshold plasma rivaroxaban level of 75 ng/mL were 95% (95% CI: 85.4%-100%) and 87.5% (95% CI: 71.3%-100%), respectively, in real-world clinical situations. Plasma rivaroxaban level of threshold level of 75 ng/mL can be calculated from prediction formula by INR value with satisfactory accuracy and it can be used to guide the decision for reversal.

Dynamics of RAS Mutations in Liquid Biopsies in Metastatic Colorectal Cancer Patients-Case Series and Literature Review.

Liquid biopsies can accurately identify molecular alterations in patients with colorectal cancer with high concordance with tissue analysis and shorter turnaround times. Circulating tumor (ct) DNA analysis can be used for diagnosing and monitoring tumor evolution in patients with metastatic colorectal cancer who are treated with EGFR inhibitors. In this article, we reported three clinical cases to illustrate the relevance of RAS mutations identified in ctDNA samples of patients with wild-type metastatic colorectal cancer who received an EGFR inhibitor plus chemotherapy as first-line treatment. The identification of RAS mutations in these patients is one of the most frequently identified mechanisms of acquired resistance. However, detecting a KRAS mutation via liquid biopsy can be caused by inter-tumor heterogeneity or it can be a false positive due to clonal hematopoiesis. More research is needed to determine whether ctDNA monitoring may help guide therapy options in metastatic colorectal cancer patients. We performed a literature review to assess the technologies that are used for analysis of RAS mutations on ctDNA, the degree of agreement between tissue and plasma and the importance of tissue/plasma discordant cases.

Comparison of sample materials for S100b analysis

Head injury is a potentially lethal and frequently occurring condition in the emergency department (ED). Reliable and fast diagnosis is important both for patients and flow in the ED. Circulating S100B is used to rule out the need for head computer tomography in low-risk patients with mild head injury. The flow of these patients through the ED would benefit from shorter turn-around time. Standard serum clotting tubes require 30-60 min clotting time, followed by an analysis time of 45 min. Here, we evaluated the performance of two alternative blood collection tubes; a rapid serum tube (RST) with a recommend clotting time of 5 min and a hirudin tube (HIR) for instant anticoagulation. S100B measurement was performed on paired blood samples from 221 subjects using a Roche Cobas 602 analyser. The performances of the alternative tubes were evaluated by method comparison to the standard serum clotting tube, repeatability and agreement of results obtained from alternative tubes compared with the standard clotting tube. Both alternative tubes had a minor positive bias (RST = 0.011 µg/L, HIR = 0.008 µg/L). The repeatability was 2% for RST and 10% for HIR, while being 4% for the standard clotting tube. In the agreement analysis, the positive and negative predictive values for RST were 62% and 100% while being 73% and 99% for HIR respectively. Our study suggests that RST is a feasible alternative to reduce laboratory turn-around time in S100b analysis.