Prolonged Turnaround Time Research Articles

CHAMP: A Centrifugal Microfluidics-Based CRISPR/Cas12b-Combined Real-Time LAMP One-Pot Method for Mycoplasma pneumoniae Infection Diagnosis.

The Mycoplasma pneumoniae outbreak poses health risks to community residents. However, it still has limitations for current clinical diagnostic methods (qPCR nucleic acid assay or IgM immunoassay), including specialized handling, expensive equipment, prolonged turnaround time, and false positives and negatives, highlighting the need to improve clinical diagnostic methods. Herein, we present a novel centrifugal microfluidics-based method for rapidly diagnosing M. pneumoniae infections (CHAMP system). This user-friendly method combines CRISPR/Cas12b and real-time loop-mediated isothermal amplification (LAMP) in a one-pot reaction, offering high sensitivity, specificity, and simplicity for methodology. By adding fully automated nucleic acid magnetic bead-extracted samples to a prepackaged centrifugal microfluidics chip, 48 samples can be automated tested simultaneously within 15 to 60 min at 60 °C. 427 clinical nasopharyngeal swab specimens were used for validation, demonstrating good positive and negative predictive values and good diagnostic sensitivity, specificity, and significant time savings. This method is particularly suitable for detecting low nucleic acid copies of M. pneumoniae samples.

New methods to detect bacterial or viral infections in patients with chronic obstructive pulmonary disease.

Patients with chronic obstructive pulmonary disease (COPD) are frequently colonized and infected by respiratory pathogens. Identifying these infectious etiologies is critical for understanding the microbial dynamics of COPD and for the appropriate use of antimicrobials during exacerbations. Traditional methods, such as bacterial and viral cultures, have been standard in diagnosing respiratory infections. However, these methods have significant limitations, including lack of sensitivity and prolonged turnaround time. Modern molecular approaches offer rapid, sensitive, and specific detection, though they also come with their own challenges. This review explores and evaluates the clinical utility of the latest advancements in detecting bacterial and viral respiratory infections in COPD, encompassing molecular techniques, biomarkers, and emerging technologies. In the evolving landscape of COPD management, integrating molecular diagnostics and emerging technologies holds great promise. The enhanced sensitivity of molecular techniques has significantly advanced our understanding of the role of microbes in COPD. However, many of these technologies have primarily been developed for pneumonia diagnosis or research applications, and their clinical utility in managing COPD requires further evaluation.

Enhanced Detection of Klebsiella Pneumoniae Using Electric-Double-Layer FET Sensor: Rapid, Temperature-Boosted Probe-Target Binding Analysis

Klebsiella pneumoniae demonstrates versatility in its pathogenicity, leading to diverse infections in humans such as pneumonia, urinary tract infections, bacteremia, wound infections, meningitis, endocarditis, and sepsis. The severity of these infections is contingent upon the patient's immune status, the site of infection, and the existence of underlying medical comorbidities. A sputum or urine culture, on the other hand, typically takes between 24 and 72 hours to produce results. Over recent years, various innovative methodologies have emerged, including optical and electrochemical techniques and molecular detection via PCR. Despite the diversity of available techniques, concerns persist regarding their sensitivity and specificity. Moreover, fluorescence-based methodologies and Surface Plasmon Resonance (SPR)-based sensors have been explored for bacterial detection. However, these existing methods have drawbacks such as elevated costs, prolonged turnaround times, the need for sophisticated instrumentation, and a demand for skilled personnel. Field-effect transistor (FET) sensors have garnered considerable scientific attention since their inception due to their remarkable sensitivity, facile signal readout, and the capability for label-free assays. The aim of this research is to detect the detect Klebsiella pneumoniae bacteria in blood serum by double electric layer (EDL) extended-gate field-effect transistor (FET) sensor. In this study, a preliminary investigation employed a single-step surface functionalization approach to immobilize receptor probes, specifically single-stranded DNA (ssDNA). This strategy aimed to enable the rapid detection of complementary DNA (cDNA) across varying concentrations, leveraging differential gate voltages to modulate the sensitivity of this analytical platform. The designed probes were successfully immobilized onto a disposable chip housing a pair of gold electrodes. A handheld reader, integrating enhancement-mode N-channel MOSFETs, established connectivity with a laptop via a USB port to facilitate the measurement of sensor signals. By applying pulsed gate voltage to the input electrode, which modulates the channel conductivity which behaves as a function of the charge distribution within the EDL structure, consequently influencing the drain current of the MOSFET. The immobilized probe, positioned on the gate electrode, underwent testing using varying concentrations of cDNA introduced into TE buffer. Detection of probe-target binding occurred through fluorescence alterations and electrically by assessing changes in drain current. In order to improve the response time, we elevated the temperature near the Tm enhances sensitivity and binding rates, in shorter time period of 1 minutes. Figure 1

EGFR mutation testing trends for patients with metastatic, non-squamous non-small cell lung cancer (non-SQ NSCLC) in Queensland, Australia from 2014-2021.

e13505 Background: Lung cancer is the leading cause of cancer-related mortality worldwide. Epidermal growth factor receptor (EGFR) is the most common actionable mutation in non-small cell lung cancer (NSCLC) with routine testing recommended globally. In late 2013, screening for EGFR mutations was publicly funded in Australia for metastatic non-SQ-NSCLC. However, timely EGFR results are not universally available, often limited by tissue quantity/quality or prolonged turnaround times. This in turn affects access to treatment and thus survival. Methods: We aimed to examine the rates of EGFR testing over time and explore factors impacting results. Cases were identified from the Queensland Oncology Repository, a clinical database consolidating diagnostic, treatment and outcome data for all Queenslanders with cancer through the Queensland Cancer Registry. Cases were included if they had metastatic non-SQ-NSCLC, EGFR testing available via Pathology Queensland, and no other metastatic solid organ cancer within 1 year. Primary outcomes were EGFR mutation testing rates and time from first biopsy to EGFR mutation result, stratified by year of diagnosis and rurality. Results: A total of 3369 cases were included, of which 2871 had EGFR testing. The EGFR mutant (mt) rate was 12.6%, while 16.1% of cases had no EGFR results. Of cases without a conclusive EGFR result, reasons included: 179 transitioned to best supportive care before testing, 208 with insufficient tissue for a conclusive result, and 155 without testing for unclear reasons. The average time from biopsy to EGFR result improved from 29.9 days in 2014 to 21.5 days in 2021, with no significant difference in time to result between major cities, regional or remote areas. Cases with no EGFR results were more prevalent in rural areas. The proportion of patients living in outer regional/remote areas with no EGFR result was 21.1% compared to 15.5% in those living in major cities/inner regional sites. This was a relative increase of 36.2% (95% CI: 10.1% - 68.6%), a significant result (χ2 = 7.7483, p=0.005). Cases with no EGFR results in outer regional and remote sites declined from 30.1% in 2014-2015 to 15.3% in 2020-2021. Conclusions: EGFR mutation testing and result time has improved since 2014. Though time to result was not affected by rurality, significantly more rural patients lacked conclusive EGFR data, highlighting a gap in access to care. The cumulative EGFR no result rate of 16% and result time of 24 days indicates health systems need to more rapidly adapt to new treatment paradigms, particularly in the era of targeted therapies. [Table: see text]

Facilitators and barriers to optimum uptake of multimonth dispensing of antiretroviral treatment in Morogoro, Tanzania: a qualitative study

ObjectivesAimed at determining facilitators and barriers to optimum uptake of multimonth dispensing (MMD) of antiretroviral treatment (ART).DesignQualitative study conducted through in-depth interviews.SettingAn explorative qualitative approach conducted at three high-volume care...

Streamlining School Registration: An Innovative Automated System for Registrars

Traditionally, educational institutions, such as Government and Public High Schools, have relied on manual procedures to manage learners' Permanent Records and Report Cards. These manual processes involve cumbersome paperwork, extensive data entry, and prolonged turnaround times for requests and issuances. However, given the evolving educational landscape and the growing demand for efficiency and accuracy, there is an urgent need to modernize these procedures. Recognizing this necessity, the Department of Education (DepEd) issued DepEd Order (DO) No. 54 s.2016, establishing standardized procedures and guidelines for requesting and issuing learners' Permanent Records and Report Cards across all public schools nationwide. This study, known as Streamlining School Registration: An Innovative Automated System for Registrars, aimed to enhance and streamline registrar processes specifically within Bagonbon National High School through automation and integration. The approach involved software development, stakeholder consultations, and usability testing. The outcomes demonstrated significant time savings, reduced errors, and increased user satisfaction. The implications suggest improved efficiency in school administration, with plans focusing on scalability and adaptability to meet the specific needs of the educational setting.

Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2024 Update by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM).

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by experts in both adult and pediatric laboratory and clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including arboviral Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also addressed. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.

Evaluation Of Surrogate Markers to Define H3 G34R/V-Mutant Gliomas

Background: H3 G34-mutant glioma was a new high-grade glioma, characterized by mutation of histone3.3 codon34. Currently, standard gene sequencing methods are helping in tumor diagnosis, but less expensive and faster H3 G34R/V staining method has not been studied yet in Thailand. Objectives: The purpose of this research is to find surrogate makers for diagnosing this tumor by uncomplicated immunohistochemical method. Methods: Formalin-fixed and paraffin-embedded tissue samples of 30 diffuse hemispheric gliomas were collected H3 G34R, H3 G34V, Olig2, p53 were evaluated using immunohistochemistry. Comparisons of immunohistochemical method and sequencing standard technique were made. Cost-effectiveness was analyzed. Results: Two cases of H3 G34-mutant gliomas were confirmed by mutation analysis. One case was positive for H3 G34V antibody (1/1) while another case was negative for H3 G34R (0/1). The cost-effectiveness showed that the sequencing technique prolonged turnaround time but gave a cost saving 23 USD (17%). Conclusions: G34R and G34V antibodies are not sensitive surrogate markers for diagnosing H3.3 G34-mutant gliomas. However, more samplings are yet to be tested in the future.

Assessment of hematology laboratory performance in the total testing process using quality indicators and sigma metrics in the northwest of Ethiopia: A cross-sectional study.

Assuring laboratory quality by minimizing the magnitude of errors is essential. Therefore, this study aimed to assess hematology laboratory performance in the total testing process using quality indicators and sigma metrics. A cross-sectional study was conducted from April to June 2022. The study included a total of 13,546 samples. Data on included variables were collected using a checklist. Descriptive statistics were used to present the overall distribution of errors. Binary logistic regression models were applied. Furthermore, using a Sigma scale, the percentage of errors was converted to defects per million opportunities to assess laboratory performance. Finally, the defect per million opportunities was converted to a sigma value using a sigma calculator. Of the 13,546 samples and corresponding requests, the overall error rate was 123,296/474,234 (26%): 93,412/47,234 (19.7%) pre-analytical, 2364/474,234 (0.5%) analytical, and 27,520/474,234 (5.8%) post-analytical. Of the overall errors, 93,412/123,296 (75.8%), 2364/123,296 (1.9%), and 27,520/123,296 (22.3%) were pre-analytical, analytical, and post-analytical errors, respectively. The overall sigma value of the laboratory was 2.2. The sigma values of the pre-analytical, analytical, and post-analytical phases were 2.4, 4.1, and 3.1, respectively. The sample from the inpatient department and collected without adherence to the standard operating procedures (SOPs) had a significantly higher (p < 0.05) rejection rate as compared to the outpatient department and collected with adherence to SOPs, respectively. In addition, an association between prolonged turnaround times and manual recording, inpatient departments, and morning work shifts was observed. The current study found that the overall performance of the laboratory was very poor (less than three sigma). Therefore, the hospital leadership should change the manual system of ordering tests and release of results to a computerized system and give need-based training for all professionals involved in hematology laboratory sample collection and processing.

Are tube fill volumes below 90% a rejection criterion for all coagulation tests?

Rejected samples lead to prolonged turnaround time and delayed diagnosis and treatment of patients. This study was conducted to determine minimum acceptable sample volume in Sarstedt brand coagulation tubes to reduce high sample rejection rate. Blood samples were drawn from 20 participants (10 healthy volunteers and 10 patients receiving oral anticoagulant) into coagulation tubes. Six samples were taken from each participant, with tube fill volumes of 100%, 90%, 80%, 70%, 60%, and 50%. Prothrombin time (PT), active partial thromboplastin time (aPTT), and fibrinogen tests were analyzed. According to quality performance specifications, the tube fill volume must be at least 70% for PT and aPTT and 50% for fibrinogen. There was no statistical difference in samples from healthy volunteers for PT, aPTT, and fibrinogen tests when the minimum tube fill volume was at least 80%, 90%, and 50%, respectively. These percentages were 50%, 70%, and 60%, respectively, in patients receiving oral anticoagulant. Sarstedt tubes meet quality standard specifications at a 70% fill rate for PT and aPTT and a 50% fill rate for fibrinogen. Comprehensive studies with larger populations are needed to accept these values as sample acceptance criteria for the laboratory.

Predicting Molecular Alterations from Blast Morphology of Acute Myeloid Leukemia Bone Marrow Aspirate Smears Using Machine Learning

Introduction Acute Myeloid Leukemia (AML) has enormous molecular and cytogenetic heterogeneity. Evaluation of bone marrow morphology is essential in the diagnosis of AML, however, it requires significant training and there is wide inter-observer variability. Genomic testing has been progressively relied on for AML classification, ultimately helping to dictate prognosis and guide clinical management. However, genomic testing, if performed, can be subject to prolonged turnaround times and lacks clinical penetration in low-resource settings. To overcome these challenges, we aimed to evaluate the feasibility of predicting clinically relevant genomic alterations from bone marrow cell morphology using a machine learning approach. Methods We scanned 799 Wright-stained bone marrow aspirate smear slides, made for routine patient care, for subjects diagnosed with AML. These subjects were linked to clinical data, including pertinent cytogenetic/molecular alterations and subclassified as cases with mutated Nucleophosmin 1 ( NPM1), those with TP53 mutations and those with myelodysplastic-related changes (AML-MRC). Whole slide images were screened for containing spicules and blasts, and were analyzed to detect 180 million cells (blasts and non-blasts) excluding hemodilute and particle regions. We developed a multi-instance model to predict patient molecular subtype by repeatedly sampling 512 cells from each slide and using these to train a classifier that weights cells with morphology relevant to subtype. We also trained a model to predict NPM1 and TP53 mutations independently, as well as other frequent variants reported to impact blast morphology. Results Performance in predicting NPM1/TP53/AML-MRC subtype was moderate (0.80 AUROC). Performance of the single-gene model varied, with NPM1 having the highest performance (0.85 AUROC) followed by IDH (0.80 AUROC), FLT3 (0.79 AUROC) and TP53 (0.62 AUROC). Conclusions This study provides promising preliminary results for prediction of genetic alterations in AML in a large-scale single-institution dataset. Interestingly, this method did not rely on the classification of individual cells, avoiding the need for manually collecting annotations to train a blast cell classifier. Future work will evaluate the morphology of cells attended by the multi-instance model, and explore the value of enriching sampled cells with blasts using cell classification methods.

814. Impact of Testing Turnaround Times on Clinical Outcome in Hospitalized Patients with Histoplasmosis and Blastomycosis

Abstract Background Patients (pt) with histoplasmosis (histo) and blastomycosis (blasto) requiring hospitalization have unacceptably high mortality rates. In part, this is due to a delay in diagnosis. Serum (S) and urine (U) antigen (Ag) testing are often crucial for timely antifungal therapy. Clinical observations suggested delays in ordering samples to be sent to reference labs upon admission and prolonged turnaround time (TAT) for test results can lead to delays in starting therapy and poor outcomes. We sought to determine the impact of TAT for histo and blasto Ag testing on clinical outcomes of hospitalized patients (pt) at our institution. Methods Retrospective evaluation of all adult inpatients with histo or blasto diagnosed by positive U or S Ag tests from 1/1/15-12/31/22 was conducted. TAT from admission to result (TAT-AR) and from sample collection to result (TAT-CR) for the earliest positive test were calculated. Clinical data, including treatment &amp; outcomes were collected. Only pt who received antifungal therapy or had a postmortem diagnosis were included. The relationship between TAT-AR and TAT-CR and outcome was evaluated. Results Of 39 pt (mean age 47±19 yr), 26 (67%) were men and 33 (85%) were immunocompromised: solid organ transplant recipients, 15; hematologic malignancy, 3; autoimmune/inflammatory disease on treatment, 12; others, 3. Thirty-five pt had pulmonary (8) or disseminated histo (27); 4 had disseminated blasto. Nine pt (23%) died within 4 months of diagnosis, including 8 pt with histo and 1 with blasto. Mean TAT-AR for these 9 deceased pt was 14.7± 19.5 days (d) vs 6.1±3.1 d for 30 survivors (p=.02). Mean TAT-CR for these 9 deceased pt was 5.4±1.5 d vs 3.9±1.3 d for 30 survivors (p=.003). Of the 32 pt who required IV amphotericin B (29) or died before any antifungal therapy was given (3), mean TAT-CR was 5.4±1.5 d for those who died vs 3.7±1.1 d for those who survived (p=.0013). ICU transfers, 30-d readmissions, and length of stay were not impacted by TAT-AR or TAT-CR. Conclusion Delays in TAT for initiating testing and obtaining results were associated with increased mortality of hospitalized pt with newly diagnosed histo or blasto. These findings highlight the importance of early testing and timely test results to guide treatment for hospitalized pt with these diseases. Disclosures Marisa H. Miceli, MD, Astellas: Advisor/Consultant|F2G: Grant/Research Support|Scynexis: Advisor/Consultant|Scynexis: Grant/Research Support

Clustered Regularly Interspaced Short Palindromic Repeats-Based Diagnostics and COVID-19; A Leap Forward in Molecular Pathology

With emergence of COVID-19 threats various diagnostic strategies have also surfaced. Conventionally, the laboratory world used to rely on serological diagnosis but availability of molecular techniques, especially “Polymerase Chain Reaction” (PCR) has initially emerged as the front line test for diagnosing SARS-CoV2 infection. Though defined as the current mainstay of COVID-19 diagnosis, still the technology suffers with less diagnostic sensitivity and specificity along with prolong Various diagnostic strategies have also surfaced with the emergence of the COVID-19 threat. Conventionally, the laboratory world used to rely on serological diagnosis, but the availability of molecular techniques, especially “Polymerase Chain Reaction” (PCR), has initially emerged as the front-line test for diagnosing SARS-CoV2 infection. Though defined as the current mainstay of COVID-19 diagnosis, the technology still suffers from less diagnostic sensitivity and specificity and prolonged turnaround times (TAT). The recent emergence of novel techniques, i.e., CRISPR/Cas technologies, in diagnosing COVID-19 infection has been tremendous and provides newer replacements for PCR testing. CRISPR with Cas12 and Cas13 from CRISPR type-V and type-VI has the potential to revolutionize COVID-19 diagnosis due to better diagnostic efficiency, lower limits of detection (LOD), much-reduced turnaround times (TAT) and availability as point of care testing (POCT). Key technologies discussed in this include SHERLOCK, DETECTER, AIOD-CRISPR, PAC-MAN, CREST and others. This short communication briefly conceptualizes CRISPR/Cas, followed by a discussion on currently available CRISPR technologies for COVID-19 infection with an overview classification of most available methods.

Improving Turnaround Time for the Issue of Blood Components in Case of Emergency

Background and Objectives: During a surgical or medical emergency, the timely issue of crossmatched blood is crucial for efficient and satisfactory patient revival. Turnaround time (TAT) is the duration taken from the time blood requests, and samples are received in the blood center until the blood is crossmatched and available for blood transfusion. The study aimed to audit the TAT in our center, analyze and study the factors delaying TAT, and formulate plans to improve it by implementing corrective measures. These actions would directly or indirectly impact the outcomes of the delivery of patient care in emergency services. Methods: A record-based prospective study was performed in a tertiary care teaching hospital with trauma and all emergency services in Southwestern India. TAT was calculated for all emergency blood requests received over 16 months in a systematic sampling method. Cases with prolonged TATs, where the product issue TAT exceeded the internal policy and quality indicator standards (15 min for emergency packed red blood cells issue), were further evaluated for causes of delay and analyzed at frequent intervals. Results: The mean TAT at the start of the study was 17.1 min (standard deviation [SD] 1.05 min), gradually reducing to 14.9 min (SD 0.62 min) by the end of the study, and it was statistically significant with P = 0.01. Conclusion: It is essential to deduce the causes for delayed TAT and work on those variables amenable to modifications based on priority to improve the TAT regarding pretransfusion testing and the issue of blood products, which is crucial in emergency services.

Turnaround time of tissue next generation sequencing in cancer patients at a safety net hospital: A quality improvement project.

e18707 Background: Tissue Next Generation Sequencing (NGS) testing can identify targetable genetic alterations, and has become an essential component of cancer care. Prolonged turnaround time (TAT) for tissue NGS testing (time from ordering until report arrival) can be a barrier for optimal treatment. Reducing the TAT can significantly aid the decision making process and improve the time to treatment initiation. As a quality improvement project, we explored a strategy to improve the TAT at our safety net hospital. Methods: We studied the TAT of commercial NGS test (FoundationOne CDx) ordered between January and December of 2022 by the oncology service at Bellevue Hospital Center (BHC), an affiliated public hospital. Tissue NGS testing was ordered for solid tumors regardless of tumor origin at the discretion of the provider. During the first half of the year, specimens prepared at BHC lab were manually dropped off at a central location for shipping to Foundation Medicine lab (testing site). The workflow was changed on 7/7/2022 to introduce a courier system to pick up the specimens from pathology lab at BHC. We analyzed the data reported by Foundation Medicine. Results: As of 2/1/2023, all specimens ordered between 1/1/2022 to 12/29/2022 were reported. There were 123 reports, of which 122 were used for the analysis. 1 report was excluded due to mislabelling of the specimen at the testing site that led to significant delay in TAT. The mean TAT of all reported specimens for the year 2022 was 23 days. Introduction of the courier reduced the mean TAT from 25 days to 20 days. After introducing the courier system, the mean time for specimen analysis was similar, but the mean time from specimen ordering to arrival at the testing site was reduced from 14 days to 10 days. Conclusions: The TAT for tissue NGS testing in underserved cancer patients at a safety net hospital can be successfully improved by implementing a courier system. The improvement was achieved regardless of tumor origin or patients’ financial ability to pay and can aid decision making for treatment initiation. This strategy can be adopted by community hospitals without access to on-site NGS testing. We are exploring additional interventions to optimize the workflow to further reduce the TAT. [Table: see text]

Addressing barriers to increased adoption of DPYD genotyping at a large multisite cancer center.

To describe the implementation of an in-house genotyping program to detect genetic variants linked to impaired dihydropyrimidine dehydrogenase (DPD) metabolism at a large multisite cancer center, including barriers to implementation and mechanisms to overcome barriers to facilitate test adoption. Fluoropyrimidines, including fluorouracil and capecitabine, are commonly used chemotherapy agents in the treatment of solid tumors, such as gastrointestinal cancers. DPD is encoded by the DPYD gene, and individuals classified as DPYD intermediate and poor metabolizers due to certain genetic variations in DPYD can experience reduced fluoropyrimidine clearance and an increased risk of fluoropyrimidine-related adverse events. Although pharmacogenomic guidelines provide evidence-based recommendations for DPYD genotype-guided dosing, testing has not been widely adopted in the United States for numerous reasons, including limited education/awareness of clinical utility, lack of testing recommendations by oncology professional organizations, testing cost, lack of accessibility to a comprehensive in-house test and service, and prolonged test turnaround time. Based on stakeholder feedback regarding barriers to testing, we developed an in-house DPYD test and workflow to facilitate testing in multiple clinic locations at Levine Cancer Institute. Across 2 gastrointestinal oncology clinics from March 2020 through June 2022, 137 patients were genotyped, and 13 (9.5%) of those patients were heterozygous for a variant and identified as DPYD intermediate metabolizers. Implementation of DPYD genotyping at a multisite cancer center was feasible due to operationalization of workflows to overcome traditional barriers to testing and engagement from all stakeholders, including physicians, pharmacists, nurses, and laboratory personnel. Future directions to scale and sustain testing in all patients receiving a fluoropyrimidine across all Levine Cancer Institute locations include electronic medical record integration (eg, interruptive alerts), establishment of a billing infrastructure, and further refinement of workflows to improve the rate of pretreatment testing.

5610480 TRANSFORMATION OF THALASSAEMIA GENETIC TESTING BY THE IMPLEMENTATION OF NGS-BASED THALASSEMIA ASSAY

Background: The haemoglobinopathies, are the most common monogenic diseases worldwide, and have been recognized as a growing global health challenge. Thalassemia is a serious health problem in Cyprus where 12 % of the population are carriers of beta-thalassaemia and about 19% are carriers of alpha-thalassaemia[1]. Because of the high incidence of the disease and the heavy impact on the health care system, the Cyprus National Prevention Programme was initiated and is successfully running since 1978. The traditional strategy for thalassaemia molecular diagnosis was designed either to identify only the most common mutations, or to target the main causing genes of thalassaemia, HBA, and HBB by conventional molecular techniques such as PCR, Real-Time PCR, MLPA, Sanger sequencing, and Mini sequencing. The complex analysis with the use of multiple different techniques to obtain a result, can cause prolonged turn-around times and costly processes and may even not be conclusive. Aim: The aim is to replace the laborious conventional molecular testing with a comprehensive analysis of the thalassaemias by the establishment of an NGS-based test for the simultaneous genetic analysis of all variants on both HBA and HBB gene clusters. Methods: A commercial CE-IVD NGS Thalassemia kit, that detects all sequence variants in HBA1, HBA2, and HBB in a single run was evaluated. The assay detects SNVs, and Indels and also uses two independent methods in parallel to detect CNVs. For the initial evaluation, 25 DNA samples with known genotypes, previously characterised in our lab, were used. For the validation study, 100 DNA samples were analysed using the NGS Thalassemia kit in parallel with the conventional molecular methods. The results obtained were assessed and compared. Results: The initial evaluation of the NGS thalassemia assay demonstrated the strength of the assay to accurately detect all variations in the analysed genes. Moreover, the assay also detected variations that were not previously identifiable by our conventional multi-method strategy, Thus, we demonstrated the ability of the assay for complete analysis of thalassaemia. The assay was successfully validated: the results obtained by the NGS assay were in complete concordance with results from parallel analysis by our standard strategy. Hence, the NGS Thalassemia kit was successfully implemented in our daily routine practice. Summary/conclusion: The implementation of the NGS Thalassemia kit allows for comprehensive analysis for the haemoglobinopathies in a single run. It is very efficient compared to our traditional previously conducted thalassemia testing, yielding results of unprecedented quality, as well as saving time on three levels - for the physician, for the lab, and most importantly for the patient. Reference 1. Kountouris, P., et al, Scientific reports, 2016.6: p. 26371.

Implementation of microsatellite instability testing for the assessment of solid tumors in clinical practice.

In Japan, microsatellite instability (MSI) testing for solid tumors was introduced in clinical practice in December 2018. Although immune checkpoint inhibitors (ICIs) are established standards of care for patients with MSI-high tumors, the status of implementing MSI testing in clinical practice remains unclear. We retrospectively reviewed the medical records of patients with solid tumors who underwent MSI testing between January 2019 and December 2020 at our institution. In total, 1,052 MSI tests were performed in 1,047 patients. Regardless of specimen volume and condition, the MSI status was successfully determined in 1,041 (99.0%) tests, encompassing 27 tumor types (microsatellite stable [MSS] or MSI-low: n=991 [95.2%] and MSI-high: n=50 [4.8%]). Patients whose specimens were fixed with 20% neutral buffered formalin (NBF) and who had specimens with prolonged storage (98.4% and 95.4%) showed lower success rates than those whose specimens were fixed with 10% NBF and who had specimens with nonprolonged storage (100.0% and 99.6%), respectively. The prolonged turnaround time (TAT) in MSI-high cases (median TAT: 24 days) was a critical issue that directly resulted in treatment delay. Of the 50 patients with MSI-high tumors, 24 (48.0%) received ICIs and 34 (68.0%) were referred to the Department of Clinical Genetic Oncology where 6 (12.0%) patients were diagnosed with Lynch syndrome. MSI testing was successfully performed for various types of tumors and specimens in clinical practice. Our study results identified certain issues associated with the clinical implementation of MSI testing, including optimal specimen selection, extended TAT in MSI-high cases, and awareness of hereditary tumors.

Quality of Medical Care at the Emergency Departments of Public Hospitals in Kenya

Globally, states are obliged to prioritize quality medical care at emergency departments (EDs). Kenya is not an exception since medical care services are mainly offered in the outpatient departments. However, the quality of care in these outpatient departments has not been evaluated. The aim of this study was to investigate quality of care at EDs of public hospital in Kenya, with a focus on Bungoma County. The study evaluated the availability of infrastructure, equipment, supplies and personnel. Besides, the researcher assessed processes, protocols, and outcomes of care at the Eds in Kenya’s public hospitals. A cross-sectional study design was employed, with a sample of 10 ED in-charges and 398 patients. The participants were proportionately recruited from the EDs via probability proportional to size (PPS). Quality of the EDS was measured using the Donabedian model with structure assessed by evaluating availability of infrastructure, equipment, supplies and personnel for emergency care. Process was evaluated by measuring turnaround timelines, assessment of presence and utilization of triage systems, protocols, and guidelines. Outcomes were measured using number of admissions, deaths, left without being seen, unplanned re-attendance, and patient service experience. Data collection was based on WHO observation checklists and with the help of questionnaires. The analysis consisted of descriptive and inferential statistics. The findings revealed that infrastructure availability was 42.0% with all EDs lacking resuscitation rooms and high dependency units. Secondly, imaging rooms were in 40% of the hospitals, blood banks in 50%, and running water in 70%. Third, equipment availability was 34.7% with oxygen source, pulse oximeter, point of care ultrasound and trauma cart being available in 10%. Fourth, regular maintenance of equipment was in 52.5% of the EDs. Finally, availability of supplies for resuscitation was 52% with Supplies for airway management being the least (22%). From the study, it was apparent that trained personnel, equipment, supplies and processes such of triage systems. This has contributed to prolonged turnaround time and high re-attendance rates. There is need for provision of adequate infrastructure, equipment, personnel, and systems for emergency care in public hospitals EDs in Bungoma County to improve quality of care.

Comparison of the BioFire Joint Infection Panel to 16S Ribosomal RNA Gene-Based Targeted Metagenomic Sequencing for Testing Synovial Fluid from Patients with Knee Arthroplasty Failure.

The diagnosis of periprosthetic joint infection (PJI) is challenging, often requiring multiple clinical specimens and diagnostic techniques, some with prolonged result turnaround times. Here, the diagnostic performance of the Investigational Use Only (IUO) BioFire Joint Infection (JI) Panel was compared to 16S rRNA gene-based targeted metagenomic sequencing (tMGS) applied to synovial fluid for PJI diagnosis. Sixty synovial fluid samples from knee arthroplasty failure archived at -80°C were tested. Infectious Diseases Society of America (IDSA) diagnostic criteria were used to classify PJI. For culture-positive PJI with pathogens targeted by the JI panel, JI panel sensitivity was 91% (21/23; 95% confidence interval [CI], 73 to 98%), and tMGS sensitivity was 96% (23/24; 95% CI, 80 to 99%) (P = 0.56). Overall sensitivities of the JI panel and tMGS for PJI diagnosis were 56% (24/43; 95% CI, 41 to 70%) and 93% (41/44; 95% CI, 82 to 98%), respectively (P < 0.001). JI panel and tMGS overall specificities were 100% (16/16; 95% CI, 81 to 100%) and 94% (15/16; 95% CI, 72 to 99%), respectively. While the clinical sensitivity of the JI panel was excellent for on-panel microorganisms, overall sensitivity for PJI diagnosis was low due to the absence of Staphylococcus epidermidis, a common causative pathogen of PJI, on the panel. A PJI diagnostic algorithm for the use of both molecular tests is proposed.