Turnaround Time Research Articles

Subclavian vessels injury: An underestimated complication of clavicular fractures

Clavicle fractures are frequent orthopedic injuries, often resulting from direct trauma or a fall. Most clavicle fractures are treated conservatively without any complications or adverse effects. Concomitant injuries of the subclavian vein or artery are rarely encountered and most commonly associated with high-energy trauma or comminuted clavicle fractures. They are potentially life-threatening conditions leading to hemorrhage, hematoma, pseudoaneurysm or upper limb ischemia. However, the clinical presentation might be obscure and easily missed, particularly in closed and minimally displaced clavicular fractures, and timely diagnosis relies on early clinical suspicion. Currently, computed tomography angiography has largely replaced conventional angiography for the assessment of subclavian vessel patency, as it demonstrates high accuracy and temporal resolution, acute turnaround time, and capability of multiplanar reconstruction. Depending on the hemodynamic stability of the patient and the severity of the injury, subclavian vessel lesions can be treated conservatively with observation and serial evaluation or operatively. Interventional vascular techniques should be considered in patients with serious hemorrhage and limb ischemia, followed by stabilization of the displaced clavicle fracture. This review aims to provide a comprehensive overview of the incidence, clinical presentation, diagnostic approaches, and current management strategies of clavicle fractures associated with subclavian vessel injuries.

Point-of-care testing improves care timeliness in the emergency department. A multicenter randomized clinical trial (study POCTUR).

Emergency department (ED) crowding is a widespread problem that positions patients at risk. The desire to improve the ED throughput requires novel approaches. Point-of-care testing (POCT) has emerged as useful technology that could contribute to create more efficient patient flow and better timeliness in the ED. The main objective of our study is to demonstrate, in a multicenter study, that POCT benefits care timeliness in the ED. We conducted a multicenter and cluster randomized study. A total of 3,200 patients. We randomly assigned patients to a POCT group or Central Laboratory Group. The primary outcome was the ED time to clinical decision. The secondary outcome included the length of stay and the laboratory turnaround time. Readmission within the seven after discharge was also calculated. The primary finding of this study is a strategy based on POCT that aims to significantly improve care timeliness in the ED. We found significant reductions in all outcomes regardless of presentation reason, patient disposition or hospital type. Time to clinical decision decreased by 75.2 min (205-129.8), length of stay by 77.5 min (273.1-195.6) and laboratory turnaround time by 56.2 min (82.2-26) in the POCT group. No increase in readmission was found. Our strategy represents a good approach to optimize timeliness in the ED. It should be seen as a starting point for further operational research focusing on POCT for improving throughput and reducing crowding in the ED.

The Society for Immunotherapy of Cancer Perspective on Tissue-Based Technologies for Immuno-Oncology Biomarker Discovery and Application.

With immuno-oncology becoming the standard of care for a variety of cancers, identifying biomarkers that reliably classify patient response, resistance, or toxicity becomes the next critical barrier towards improving care. Multi-parametric, multi-omics, and computational platforms generating an unprecedented depth of data are poised to usher in the discovery of increasingly robust biomarkers for enhanced patient selection and personalized treatment approaches. Deciding which developing technologies to implement in clinical settings ultimately, applied either alone or in combination, relies on weighing pros and cons, from minimizing patient sampling to maximizing data outputs, and assessing reproducibility and representativeness of findings, while lessening data fragmentation towards harmonization. These factors are all assessed while taking into consideration the shortest turnaround time. The Society for Immunotherapy of Cancer (SITC) Biomarkers Committee convened to identify important advances in biomarker technologies and to address advances in biomarker discovery using multiplexed immunohistochemistry and immunofluorescence, their coupling to single cell transcriptomics, along with mass spectrometry-based quantitative and spatially resolved proteomics imaging technologies. We summarize key metrics obtained, ease of interpretation, limitations and dependencies, technical improvements, and outward comparisons of these technologies. By highlighting the most interesting recent data contributed by these technologies, and by providing ways to improve their outputs, we hope to guide correlative research directions and assist in their evolution towards becoming clinically useful in IO.

A Day Saved is a Life Saved: Direct Antimicrobial Susceptibility Testing from Positively Flagged Blood Culture Bottles and their Concordance with the Routine Method.

Sepsis is a major health problem worldwide and is associated with high morbidity and mortality with every hour delay in initiation of therapy. A conventional method of blood culture and Antimicrobial Susceptibility Testing (AST) takes around 48-72 hours. Empirical antibiotics need to be administered until the sensitivity report is made available. It has been estimated that 20-50% of the empirical antibiotics are inappropriate, resulting in prolonged hospital stays, adverse effects, and emergence of drug resistance. Additionally, this also puts an extra financial burden on both the patients and healthcare settings. Performing direct Antimicrobial Sensitivity Testing (dAST) is an important tool to reduce turn-around time (TAT) by at least 18-24 hours, thus reducing morbidity and mortality among critically ill patients. Direct AST (dAST) was performed from the positively flagged blood culture bottles received between December, 2021 to May, 2022 from Intensive Care Units (ICUs) on Mueller- Hinton Agar (MHA) using four drops of withdrawn blood. dAST was performed for six drugs: Ceftriaxone-30 μg (CTR), Piperacillin/Tazobactam-100/10 μg (PIT), Meropenem-10 μg (MRP), Ciprofloxacin-5 μg (CIP), Aztreonam-30 μg (AT), and Colistin (CL). The zone of inhibition was interpreted as per CLSI M100 ed32, 2022 guidelines. A parallel conventional method was also performed to examine for categorical agreement and disagreement. Identification was carried out using MALDI-TOF MS from the colonies that appeared on the dAST plate on the subsequent day. A total of 162 positively flagged blood culture bottles were included in the study. The majority of the Gram-negative organisms were from Enterobacterales (n=109), followed by Acinetobacter spp. (n=28) and Pseudomonas aeruginosa (n=25). Out of the 972 isolate-antimicrobial combinations, overall Categorical Agreement (CA) was seen in 936 (96.3%), whereas disagreement was observed in 36 with minor error (mE) in 21 (2.2%), major error (ME) in 7 (0.7%), and very major error (VME) in 8 (0.8%) when compared to the routine method. Categorical agreement (CA) of > 99% was seen in ceftriaxone (CTR) and ciprofloxacin (CIP). In comparison, the lowest CA was observed with meropenem (MRP) at 92%. Colistin dAST was performed using the E-strip method, and the result obtained was highly convincing, with an overall disagreement of only 1.2%. Rapid dAST from positively flagged blood culture bottles proved to significantly reduce the TAT from the time of sample collection to the first availability of antimicrobial susceptibility report with excellent categorical agreement of > 95% using the conventional disc diffusion method. Results obtained were within the acceptance criteria set by U. S. Food and Drug Administration (FDA) guidelines of > 90% categorical agreement for a new method. We were able to obtain excellent concordance for colistin using the E-strip method. Performing dAST not only saves a "day", but its proper implementation would save a "life".

Real-world cost-effectiveness of multi-gene panel sequencing to inform therapeutic decisions for advanced non-small cell lung cancer: a population-based study

Multi-gene panel sequencing streamlines treatment selection for advanced non-small cell lung cancer (NSCLC). Implementation continues to be uneven across jurisdictions, partly due to uncertain clinical and economic impacts. In British Columbia (BC), Canada, the public healthcare system reimbursed a multi-gene panel in September 2016. This study determined the population-level cost-effectiveness of publicly reimbursed multi-gene panel sequencing compared to single-gene testing for advanced NSCLC. Our population-based retrospective study design used patient-level linked administrative health databases. We considered adult BC residents with a panel-eligible lung cancer diagnosis between September 2016 and December 2018. Using a machine learning approach, we conducted 1:1 genetic algorithm matching of recipients receiving multi-gene panel sequencing to controls receiving single-gene testing, maximising balance on observed demographic and clinical characteristics. Following matching, we estimated mean three-year survival time and costs (public healthcare payer perspective; 2021 CAD) and calculated the incremental net monetary benefit (INMB) for life-years gained (LYG) at conventional willingness-to-pay thresholds using inverse probability of censoring weighted linear regression and nonparametric bootstrapping. We matched 858 panel-eligible advanced NSCLC patients to controls, achieving balance for the 16 included covariates. Average test turnaround times were 18.6 days for multi-gene panel sequencing and 7.0 days for single-gene testing. After matching, mean incremental costs were $3529 (95% CI:-$4268, $10,942) and mean incremental LYG were 0.08 (95% CI:-0.04, 0.18). Among the 1000 bootstrap samples, 14.5% had lower costs and increased survival and 78.6% had higher costs and increased survival. The INMB was $523 (95% CI:-$6256, $7023) at $50,000/LYG, with a 57.5% probability of being cost-effective, and $4575 (95% CI:-$5468, $14,064) at $100,000/LYG, with an 84.0% probability of being cost-effective. Using population-based real-world data, we found a moderate to high probability that panel-based testing to inform targeted treatment for NSCLC would be cost-effective at higher thresholds. This research was supported by Genome British Columbia/Genome Canada (G05CHS) and the Terry Fox Research Institute.

City Residents Play a Pivotal Role in Managing Global Food Security While Improving Human Health and Minimizing Environmental Footprints

Background/Objectives: Improved global data allow for a new understanding of what impact the food we produce, eat and dispose of has on the environment, human health and Nature’s resources. The overall goal is to guide decision-makers and individuals by providing in-depth knowledge about the effects of their dietary preferences on human and environmental health. Methods: The method is to investigate ways to reduce environmental degradation and to secure healthy food supplies in an urbanizing world, and to quantify the options. Results: Reviewed articles show that by eating less meat-based food and more plant-based and soilless food, as well as reducing food waste and recycling urban-disposed nutrients as fertilizers, we could reduce agriculture’s land requirement by 50% to 70% while still securing a healthy food supply. Less land under cultivation and pasture would reduce global emissions to air and water to a similar extent, and allow Nature to reclaim freed areas in order to catch more carbon and rejuvenate biodiversity. Thus, we could avoid further environmental degradation such as the current clearing of new fields needed under a business-as-usual regime. Presently, some 17 million people die each year due to poor diets, which is more than double the 7 million deaths since the onset of the COVID-19 pandemic. A return to more plant-based diets with unchanged intake of proteins but less calories, sugar, salt and fat combined with less red meat and ultra-processed food would reduce foremost non-communicable diseases by up to 20% and prolong life. The article suggests that the international focus has gradually turned to the food sector’s big contribution to climate change, biodiversity loss and harmful chemicals as well as to poor human health. It argues that this century’s rapid population growth and urbanization give urban residents a pivotal role in food’s impact on agricultural areas, which today cover half of the globe’s inhabitable areas. Their food demand, rather than the activities of farmers, fishermen or loggers, will guide remedial measures to be taken by individuals, industry and the public sector. A tool to calculate the potential environmental footprints of individual or societal measures is presented. Conclusions: Measures to make the agrifood sector more sustainable are still pending full recognition in international fora such as the UN COP Summits. Smart cities fitted with infrastructures to recycle macro- and micro-nutrients and organic matter have the potential to ameliorate human-induced impacts such as emissions to air and water bodies, crossing planetary boundaries, and polluting extraction of N (nitrogen), P (phosphorus) and K (potassium). Rapid results are within reach since dietary change and the turn-around time of nutrients in food is short compared to decades or centuries for recycled materials in cars or buildings.

Robotization in microbiology.

Since 1960, Williams and Trotman had dreamed of automating all technical manipulations in bacteriology. However, this switch to automation took several decades to realize. The high cost of instruments and the attachment to classical bacteriology were the main obstacles. Automation began with blood culture incubators, and paved the way for automation in other areas of bacteriology, notably cytology, culture, identification and antibiotic susceptibility testing. Medical laboratories have been quick to recognize the efficiency of these systems and their many advantages. The reduction in turnaround times for bacteriological examinations is one of the changes that have revolutionized laboratory practice. In addition, sensitivity, safety, traceability and quality are more assured with automation. The second revolution is the integration of artificial intelligence into the processing and interpretation of bacteriological analyses. We are currently witnessing the total automation of laboratories and a reduction in human intervention. In this article, we have attempted to address all aspects of bacteriology affected by automation, and the impact of this change on current laboratory practice and quality of healthcare.

Diagnostic advances in sepsis: A comparative analysis of syndromic approaches and molecular biology techniques in clinical bacteremia

Sepsis remains a leading cause of morbidity and mortality. This retrospective study, conducted at Avicenne Military Hospital in Marrakech over ten years, analyzed 3721 blood cultures, identifying 420 cases of bacteremia (11.3% positivity rate). The predominant isolates included Staphylococcus aureus, coagulase-negative staphylococci, Escherichia coli, Klebsiella spp., and Acinetobacter baumannii, with significant resistance patterns observed. Notably, 50% of S. aureus were methicillin-resistant (MRSA), while extended-spectrum beta-lactamase (ESBL) production was found in 30% of E. coli and Klebsiella pneumoniae isolates. The FilmArray multiplex PCR system was utilized to enhance rapid pathogen identification, reducing turnaround time from 72 hours to under 2 hours, and demonstrated high concordance with conventional cultures. The molecular diagnostics identified various resistant strains, including carbapenemase-producing organisms in K. pneumoniae and multidrug-resistant A. baumannii, underscoring the critical need for effective antimicrobial stewardship. Overall, this study emphasizes the evolving epidemiology of bacteremia, the rising antimicrobial resistance, and the utility of rapid molecular diagnostics in guiding timely and appropriate treatment, ultimately aiming to improve patient outcomes in sepsis management.

New Instant Digital Pathology for EUS/EBUS Samples: The Last Advance in Bedside Diagnostics for Lung Carcinoma

Background Ex vivo fluorescence laser scanning microscopes (FCMs) allow digital tissue imaging directly from fresh, unfixed specimens without the need for conventional histological slide preparation. To date, no data have been reported on the use of FCMs in the endoscopy suite for immediate evaluation of endoscopic ultrasound (EUS)/endobronchial ultrasound (EBUS) fine needle aspiration/biopsy (FNA-B) specimens of lung lesions and/or mediastinal lymph nodes. Objectives The aim of this study was to evaluate the performance of the FCM Vivascope 2500 (Vivascope, Munich, Germany) in providing real-time adequacy assessment and diagnostic information on the digital images of fresh unprocessed EUS/EBUS FNA-B specimens and to compare it with the corresponding final histological sections of formalin-fixed and paraffin-embedded cell blocks. Methods and Results Thirty-two patients (50% male; 71 ± 8 years old) were enrolled between May 2023 and June 2024. In 28/32 (87.5%) patients, samples were defined as adequate at Vivascope evaluation, and in 20/28 (71.4%) patients, samples were classified as malignant. At final cytohistological evaluation, 87.5% of specimens were defined as adequate and 20/28 (71.4%) were diagnosed as malignant. There was perfect agreement between the Vivascope assessment of adequacy and the final cytohistological assessment on the same specimen (k Cohen 1). From a diagnostic point of view, perfect agreement was found between the two techniques in the identification of malignant neoplasms (k Cohen 1). Conclusion The use of FCM could provide rapid information on both the adequacy and malignancy of the sample obtained during EBUS tissue acquisition (EBUS-TA), with minimal or no preparation and without destroying or losing the tissue. This technique allows for obtaining representative material in EBUS/EUS for lung cancer staging and is expected to change the turnaround time from biopsy sampling to diagnostic characterization of the tumor, ultimately improving patient management both at diagnosis and at restaging in follow up.

Multicenter evaluation of Fourier transform infrared (FTIR) spectroscopy as a first-line typing tool for carbapenemase-producing Klebsiella pneumoniae in clinical settings.

Early use of infection control methods is critical for preventing the spread of antimicrobial resistance. Whole-genome sequencing (WGS) is considered the gold standard for investigating outbreaks; however, the turnaround time is usually too long for clinical decision-making and the method is also costly. The aim of this study was to evaluate the performance of Fourier transform infrared (FTIR) and artificial intelligence tools as a first-line typing tool for typing carbapenemase-producing Klebsiella pneumoniae (CPK) in the hospital setting. For this purpose, we analyzed 365 CPK isolates from two tertiary hospitals in Spain in parallel by applying unsupervised principal component analysis (PCA) and supervised algorithms (artificial neural network [ANN], support vector machine [SVM] linear, SVM radial basis function in the IR Biotyper software, and random forest in the Clover MSDAS software). Concordance with FTIR clustering considering the sequence type (ST) and the clonal cluster, obtained by cgMLST for reference purposes, was measured using the adjusted Wallace index (AWI), yielding values of 0.611 and 0.652, respectively. Different regions of the spectra were studied in relation to repeatability and reproducibility, and the polysaccharides region proved the best for FTIR differential analysis. The best results for accuracy were obtained using the ANN algorithm in the IR Biotyper software, with 80.5% of correct prediction. Regarding accuracy, the poorest results were obtained for isolates belonging to ST392 (55.5%) and the best results for ST307 (94.4%). The findings demonstrate the utility of the FTIR method as a rapid, inexpensive, first-line typing tool for detecting CPK, preserving WGS for confirmation and further characterization.

Detection of enoxaparin and argatroban by use of the novel viscoelastic coagulometer ClotPro

Owing to the simultaneous increase in the risk of thrombosis and bleeding in critically ill patients, point-of-care-available diagnostic tests to guide parenteral anticoagulation are warranted. We evaluated the detection of enoxaparin and argatroban, two commonly used parenteral anticoagulants, using the novel ClotPro viscoelastic coagulometer. For this experimental in vitro study at a tertiary care academic center, blood samples were drawn from twelve (six female, six male) healthy volunteers without intake of antithrombotic medication and no history of hemostatic disorders. Blood samples were spiked with enoxaparin (IU.ml− 1) and argatroban (µg.ml− 1) at increasing concentrations ranging from 0 to 1. The ClotPro Russell’s viper venom (RVV)-test and the ClotPro ecarin (ECA)-test clotting time were performed in parallel with conventional coagulation tests (anti-Xa activity, activated partial thromboplastin time, and diluted thrombin time). We observed a strong correlation between anti-Xa activity and the RVV-test clotting time (r = 0.88 (95% confidence interval (CI) 0.8–0.92; p < 0.001)). Although clotting time cutoff values of 71 and 145 s provided high sensitivity and specificity for detecting anti-Xa activity of ≤ 0.1 and ≥0.6 IU.ml− 1, we found a poor performance at both high and low concentrations. The ECA-test clotting time revealed a very strong correlation with activated partial thromboplastin time (r = 0.96 (95% CI 0.93–0.97; p < 0.001)) and diluted thrombin time (r = 0.97 (95% CI 0.96–0.98; p < 0.001)). The clotting time cutoff values of 86 and 298–431 s provided high sensitivity and specificity for detecting diluted thrombin time values ≤ 0.1 and 0.5-1 µg.ml− 1. Our results suggest that the RVV test is an unreliable method for monitoring enoxaparin treatment, whereas the ECA-test might be an accurate point-of-care alternative for detecting argatroban concentration with potential advantages over standard coagulation tests in terms of point-of-care applicability and turnaround time.

Development of a clinical metagenomics workflow for the diagnosis of wound infections

BackgroundWound infections are a common complication of injuries negatively impacting the patient’s recovery, causing tissue damage, delaying wound healing, and possibly leading to the spread of the infection beyond the wound site. The current gold-standard diagnostic methods based on microbiological testing are not optimal for use in austere medical treatment facilities due to the need for large equipment and the turnaround time. Clinical metagenomics (CMg) has the potential to provide an alternative to current diagnostic tests enabling rapid, untargeted identification of the causative pathogen and the provision of additional clinically relevant information using equipment with a reduced logistical and operative burden.MethodsThis study presents the development and demonstration of a CMg workflow for wound swab samples. This workflow was applied to samples prospectively collected from patients with a suspected wound infection and the results were compared to routine microbiology and real-time quantitative polymerase chain reaction (qPCR).ResultsWound swab samples were prepared for nanopore-based DNA sequencing in approximately 4 h and achieved sensitivity and specificity values of 83.82% and 66.64% respectively, when compared to routine microbiology testing and species-specific qPCR. CMg also enabled the provision of additional information including the identification of fungal species, anaerobic bacteria, antimicrobial resistance (AMR) genes and microbial species diversity.ConclusionsThis study demonstrates that CMg has the potential to provide an alternative diagnostic method for wound infections suitable for use in austere medical treatment facilities. Future optimisation should focus on increased method automation and an improved understanding of the interpretation of CMg outputs, including robust reporting thresholds to confirm the presence of pathogen species and AMR gene identifications.

The feasibility and impact of deploying a four-tests panel at antenatal care in primary health care facilities of a developing country, Kenya

IntroductionContracting HIV, syphilis, hepatitis B virus (HBV), and malaria during pregnancy significantly affects the health of the woman, the pregnancy, and the unborn child. The World Health Organization (WHO) recommends testing pregnant women for these infections to achieve triple elimination of mother-to-child transmissions. However, this goal has not been fully realized in low- to medium-income countries, primarily due to segmented testing practices. This study aimed to investigate the effect of introducing a four-tests panel on the quality of antenatal care (ANC) among pregnant women attending selected Primary Health Care facilities in Kenya.MethodsUsing a multi-design approach, we analyzed ANC medical records from 577 pregnant women attending eight facilities across four different counties. Blood from the women fingerpick was tested for HIV, Syphilis Hepatitis B Virus and Malaria using the four-tests panel and the results compared to those in the medical records.ResultsOut of 577 ANC women, only 8.3% had test results for all four infections available. The majority of the mothers had been tested for syphilis (93.7%), HIV (78.5%), and malaria (62.6%), only 19.5% had been tested for HBV. Testing the women using the 4-tests panel yielded positivity rates of 6.9% for HIV, 0.9% for syphilis, 1.9% for malaria, and 1.1% for HBV. Among those without previous test results, the positivity rate was 2.8% for syphilis, 13.8% for HIV (with 10.6% testing positive for recent p24 infections, F = 24.876, p &amp;lt; 0.001), 2.3% for malaria, and 4.5% for HBV, with 83.3% of these individuals having no prior test results. The mean positivity rate of those tested using the 4-tests panel compared to segmented single tests was significantly different. The panel was cost-effective and user-friendly for healthcare workers, and in facilities facing staff shortages, it reduced turnaround time and workloads by half. The use of the panel also improved the profiling of ANC mothers and enhanced data management for the four infections by 91.7%.ConclusionAdopting the 4-tests panel has the potential to improve test result outputs, enhance the quality-of-service delivery, and contribute significantly to the achievement of triple elimination goals.

Maximizing Laboratory Turnaround Time Efficiency: Workflow Optimization in Resource-Limited Settings

Laboratory Turnaround Time (TAT) is a critical metric in assessing the quality of laboratory services, directly impacting diagnostic speed and patient outcomes. Many laboratories in resource-constrained environments face challenges such as inefficiencies in workflow, resource limitations, and administrative redundancies, which hinder optimal TAT performance. This research aims to optimize laboratory workflow to improve TAT efficiency in a resource-constrained environment, addressing workload variability, inefficient station grouping, and administrative overlap. The research, which was conducted at the Tanah Abang Puskesmas Laboratory from May to July 2022, consisted of three stages: observation and data collection, workflow optimization, and evaluation. Interventions included task reallocation, workflow segmentation, and administrative streamlining. TAT improvement was assessed from the Complete Blood Count (CBC) and Random Blood Glucose (RBG) tests using pre- and post-intervention analysis. The results showed that after optimization, the mean TAT for the CBC test decreased significantly from 36 minutes (SD = 13.4) to 25.6 minutes (SD = 4.1), p-value &lt;0.05. For the RBG test, the TAT increased from 88.6 minutes (SD = 4.6) to 81.1 minutes (SD = 1.4), p-value &lt; 0.01. This intervention demonstrates the feasibility and effectiveness of lean management strategies in a resource-constrained environment. This research has implications for emphasizing the importance of systematic workflow optimization to improve laboratory efficiency. This research highlights practical and scalable solutions that can be adopted in similar settings globally, and future efforts should focus on integrating advanced technologies such as Laboratory Information Systems (LIS) to further improve accuracy, efficiency and patient outcomes.

Enhancing pathogens detection in suspected geriatric bloodstream infections using Nanopore-targeted sequencing.

Bloodstream infections (BSIs) in elderly patients pose substantial diagnostic and therapeutic challenges due to the limitations of traditional blood culture methods, which are hampered by slow turnaround times and false-negatives. Nanopore-targeted sequencing (NTS) emerges as a significant advancement, offering rapid and accurate pathogen detection directly from blood samples. This study demonstrates that NTS provides a higher detection rate and faster results than conventional blood cultures, crucial for the timely management of BSIs in geriatric patients, who often present with multiple or mixed infections and have poorer clinical outcomes. The findings underscore the potential of NTS to enhance diagnostic accuracy and speed, informing more effective treatment strategies and improving overall patient outcomes. Further research is essential to establish NTS as a routine diagnostic tool in the clinical management of BSIs in the elderly.

Genomic profiling and expanded use of targeted anticancer drugs in solid cancers with exhausted evidence-based treatment options (PRECODE): study protocol of a prospective, non-randomized, cohort study

BackgroundGenomic profiling of advanced solid cancer in patients with no further evidence based standard treatment options is a novel approach to identify potential experimental treatment options based on specific genomic alterations. Due to the expected short survival of these patients timely assessment of potential druggable targets is critical to minimize the risk of deterioration during the analysis.The primary objective of this prospective study is to evaluate the turnaround time for genomic profiling and the clinical investigational procedures. The secondary objectives are to investigate how often genomic alterations in tumor tissue gives rise to a matched treatment offer and evaluate the clinical outcome.MethodsThe PRECODE study is a prospective, non-randomized, single-center cohort study conducted at Departments of Oncology and Pathology, Odense University Hospital, Denmark. Enrollment between March 1, 2019 and December 31, 2024. Eligibility criteria are age ≥ 18 years, written informed consent, advanced solid tumors, exhausted treatment options, ECOG performance status 0–2, adequate organ function and life expectancy ≥ 3 months. A core needle biopsy is analyzed by next generation sequencing using a pan-cancer comprehensive panel. Results are discussed weekly at institutional/local and national multidisciplinary tumor boards.DiscussionStrategies and methods for genomic profiling of advanced solid cancers differ. Rapid analysis and interpretation of sequencing data are key to avoiding delays in initiation potential experimental treatments, as these late-stage patients may quickly deteriorate.Although a highly optimized setup with fast-track clinical evaluation and genomic profiling has been established a subset will not be offered a targeted treatment due to deterioration. Local and national multidisciplinary teams have been established to optimize individualized treatment decisions. After genomic profiling a subset of patients will take part in clinical trials, which will constrain the reporting of overall survival or progression free survival.Trial registrationDanish Ethics Committee, Projekt-ID: S-2018014, date of approval: 27- FEB- 2019) Danish Data Protection Agency (Journal no: 18/58329, date of approval: 23-NOV-2018).ClinicalTrials.gov Identifier: NCT05385081 (retrospectively registered).

Evaluation of an alternative centrifugation protocol for reducing total turnaround time

Abstract Objectives Centrifugation is a key process that should be controlled to ensure an adequate sample quality. To achieve rapid, standardized, and consistent sample centrifugation, we aimed to evaluate an alternative centrifugation protocol and its impact on the results of 20 biochemical determinations in serum. Methods The study included 45 ambulatory patients. Two serum-separating tubes were collected from each patient (Becton Dickinson (BD) Vacutainer® SST™ II Advance, 8.5 mL Ref. 366468). One of the tubes was centrifuged at 2530 × g for 10 min (control method), while the other tube was centrifuged under alternative centrifugation conditions, namely 2530 × g for 7 min. Results The analysis of results revealed that calcium, total bilirubin, and magnesium exhibited a constant and proportional systematic bias. However, considering the proportional mean difference, all analytes met the desirable bias performance established by our laboratory, except for magnesium, which met the minimum bias criteria. Conclusions Our study demonstrates that both centrifugation protocols are interchangeable for measuring the studied analytes, thereby ensuring adequate sample quality.

Field-Based cDNA-Biosensor for Accurate Detection of Canine Distemper Virus in Tissue Samples.

Canine distemper, a viral disease with a global impact on various animals including dogs, foxes, wolves, lions, and leopards, requires early diagnosis for effective treatment and outbreak control. Common laboratory methods, such as enzyme-linked immunosorbent assay, polymerase chain reaction, and viral isolation, face challenges such as extended turnaround times, high costs, and the expertise required. This study has developed a field-based biosensor for detecting the canine distemper virus (CDV), utilising a screen-printed carbon electrode (SPCE) and a computer-assisted portable potentiostat. A 30-mer oligonucleotide capture probe, designed using Primer3 Plus software version 3.3.0, detected hybridisation with the CDV complementary strand through electrochemical analysis via differential pulsed voltammetry. The developed biosensor exhibited good linearity in quantifying the target analyte concentration (0.1 to 12.8µM), with a detection limit of 0.05µM, indicating high sensitivity. Specificity tests using complementary and non-complementary sequences confirmed the biosensor's accuracy. The electrode can be reused up to eight times with a residual capacity of 93.72 ± 5.45% after regeneration using a 50mM NaOH solution. The developed biosensor was also used to detect CDV in biological samples after RNA extraction and amplification. Results from the biosensor aligned with those from reverse transcriptase polymerase chain reaction (RT-PCR) findings, showing 100% agreement. These findings support the potential development of a field-deployable portable device for effectively diagnosing canine distemper in biological samples.

Multiplex real-time PCR for detection of &lt;i&gt;qac A/B&lt;/i&gt; and &lt;i&gt;smr&lt;/i&gt; genes in Gram-positive bacteria

Background. Disinfectants are effective means of non-specific prevention of infections associated with the provision of medical care. Violation of disinfectant use regimes leads to the formation of microorganism resistance to them. To monitor the spread of clinically significant microorganisms resistant to disinfectants, the development of methods for their detection, including molecular genetic methods, remains relevant. The aim of the study was to develop a multiplex real-time PCR for the identification of qacA/B and smr genes, the determinants of resistance to cationic biocides, in Gram-positive bacteria. Materials and methods. Conserved regions of qacA, qacB and smr genes were searched, and primers and probes were designed using BLASTN, GeneRunner, and Multiple Primer Analyzer programs. To evaluate the analytical sensitivity of the multiplex PCR, plasmids pTZ57-qacA/B, pTZ57-smr, and pTZ57-16S containing qacA/B, smr and 16S rRNA gene fragments of 197 bp, 127 bp, and 287 bp, respectively, were constructed. The method was tested on clinical isolates of Gram-positive bacteria (n = 30). Results. A multiplex real-time PCR using TaqMan probes was developed for the detection of qacA/B and smr genes in Gram-positive bacteria. The 16S rRNA gene was used as an internal amplification control. The sensitivity of the multiplex PCR was 103 copies for all genes. Multiplex PCR validation showed that qacA/B genes were present in 30%, smr genes were present in 10% of the isolates tested. The reproducibility of the results was 100%. Conclusion. The developed multiplex PCR differs from existing assays by high specificity and short turnaround time, as well as by the presence of an internal amplification control. It can be used for the detection of Gram-positive bacteria potentially resistant to cationic biocides.

Molecular Identification of Etiological Agents in Fungal and Bacterial Skin Infections: United States, 2020-2024.

Background/Objectives: Cutaneous infections of fungal and bacterial origins are common. An accurate diagnosis-especially concerning pathogens that are difficult to isolate on culture-can be achieved using molecular methods (PCR) with a short turnaround time. Methods: We reviewed records of skin specimens (superficial scrapings) submitted by dermatologists across the United States with a clinically suspected dermatitis. As per physician's order, specimens were tested for infections either fungal (N = 4262) or bacterial (N = 1707) in origin. All unique specimens (one per patient) were subjected to real-time PCR assays where cases suspected of a fungal etiology were tested for dermatophytes, Malassezia and Candida, and cases suspected of a bacterial etiology were tested for Streptococcus pyogenes, Staphylococcus aureus, and the mecA gene potentially conferring β-lactam resistance. Results: Fungal agents were detected in 32.8% (SD: 4.5) of the submitted specimens, with most attributed to dermatophytes (19.3% (SD: 4.9)), followed by Malassezia (8.7% (SD: 2.8)) and Candida (2.9% (SD: 1.0)). Dermatophyte detection was more common in the elderly (≥65 years) compared to young adults (18-44 years) (OR: 1.8 (95% CI: 1.5, 2.2)), whereas Malassezia was more commonly detected in younger age groups (12.1-13.6%) than the elderly (5.6%). Candida was more frequently observed in females while dermatophytes and Malassezia were more frequently observed in males. Approximately one quarter of the submitted skin specimens tested positive for S. aureus (23.6% (SD: 3.4)), of which 34.4% (SD: 9.8) exhibited concurrent detection of the mecA gene. An S. aureus detection was more frequently observed in males (OR: 1.5 (95% CI: 1.2, 1.9)) and in children (OR: 1.7 (95% CI: 1.2, 2.5)). Streptococcus pyogenes was rarely detected. Among specimens positive for dermatophytes, 12.0% (20/166) showed co-detection of S. aureus and mecA, which is in contrast to 6.8% (70/1023) detected in samples without a fungal co-detection and 6.2% (8/130) in samples positive for Malassezia. Conclusions: PCR testing, when available, can be valuable as a part of routine care for diagnosing patients with clinically suspected skin infections. Further studies are warranted to survey the prevalence of resistant S. aureus isolates in dermatology outpatients, in particular with regard to the association with dermatophyte infections.