Laboratory Workflow Research Articles

Detection by Real-Time PCR of Helicobacter pylori and Clarithromycin Resistance Compared to Histology on Gastric Biopsies

The global rise in Helicobacter pylori (H. pylori)-related gastric complications is largely driven by increasing antimicrobial resistance and treatment failures. As a result, accurate diagnosis followed by effective treatment is crucial. We analyzed 232 gastric biopsy samples from patients undergoing endoscopy during the method validation phase, followed by 502 samples in the routine evaluation phase. Each sample was tested using the Allplex™ H. pylori and ClariR Assay on a CFX96™ real-time PCR (RT-PCR) system, with results processed through Seegene Viewer software. In the validation phase, RT-PCR results were compared to bacterial culture, while in the routine phase, they were compared to histology. The sensitivity and specificity for H. pylori detection were 100% and 96.05% (95% Confidence Interval [CI]: 93.38–98.73), respectively. For clarithromycin resistance detection, the sensitivity and specificity were 100% and 93.33% (95% CI: 84.4–100). Additionally, RT-PCR identified 11 positive samples (10.89%) that histology failed to detect. Incorporating the Allplex™ H. pylori and ClariR Assay into our laboratory workflow improved efficiency, reduced turnaround time (TaT), and proved to be more sensitive than both culture and histology combined.

Multi-year comparison of VITEK MS performance for identification of rarely encountered pathogenic Gram-negative organisms (GNOs) in a large integrated Canadian healthcare region.

This multi-year study (2014-2019) compared identification of rare and unusual Gram-negative organisms (GNOs) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (VITEK MS, bioMérieux, Laval Que.) to 16S rRNA gene sequencing (16S) according to our laboratories routine workflow; 16S is done if initial MALDI-TOF MS gave discordant, wrong, or no results. GNB isolates were first analyzed by standard phenotypic methods and MALDI-TOF MS using direct deposit-full formic acid extraction; proteomics was repeated if no result occurred. Medically approved 16S analyses were done using fast protocols. Isolate sequences were analyzed using the Integrated Database Network System (IDNS3) bacterial database (SmartGene, Lausanne, Switzerland). Three hundred thirty-one GNOs including 251 (76%) aerobic Gram-negative bacilli (GNB), 63 (19%) fastidious Gram-negative coccobacilli (fGNCBs), and 17 (5%) Campylobacterales (CAMPB) isolates were recovered from 304 specimens; >1 isolate was recovered from 19 (6%). GNOs were mainly recovered from blood cultures (31.6%) and lower respiratory specimens (43%) (one-half were isolated from cystic fibrosis patients). Accurate genus vs species identities were obtained for 67.7% and 32.5% aerobic GNBs, 73% and 60% fGNCBs, and 23.5% CAMPB (with no discrepant species), respectively. Wrong or no results were obtained for 81 (32.3%) aerobic GNBs, 17 (27%) fGNCBs, and 13 (72.2%) CAMPB. No results or misidentifications occurred for 33% of aerobic GNBs, 26% of fGNCBs, and 76.5% of CAMPB due to absence of species in the instrument's database. VITEK MS performance remained stable for aerobic GNBs and fGNCBs but improved for CAMPB with addition of Campylobacter rectus and Campylobacter curvus to the database. 16S remains important for identification of GNOs when proteomics fails.IMPORTANCEMatrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has transformed the identification of commonly encountered Gram-negative organisms (GNOs) in the clinical laboratory, but rare and unusual organisms continue to challenge the technology. This study verified performance of VITEK MS for identification of a broad range of rare and unusual clinical GNO isolates by our large reference laboratory workflow over a multi-year period. Although most GNOs were accurately identified by MALDI-TOF MS, a small number of clinical isolates (~1%-6%) required 16S sequencing for identification depending on the GNO category. Approximately one-third of aerobic Gram-negative bacilli (GNBs) and two-thirds of Campylobacterales could not be accurately identified by proteomics due to lack of an organism in the instrument's database. MALDI-TOF MS databases should be continuously updated and validated, and laboratories should have a workflow for identification of unusual or rarely encountered aerobic, fastidious, and Campylobacterales GNOs that includes 16S rRNA gene sequencing whenever proteomics cannot give a definitive identification.

Clinical Utility of Broad Range PCR for Infectious Organisms

Abstract Broad range PCR is used to identify infectious organisms when bacterial, fungal, and mycobacterial cultures are negative despite clinical evidence of infection. We performed a 6-month retrospective chart review to assess the actionability of broad range PCR and identify opportunities to improve the utility of this referral test at our institution. One hundred eleven broad range PCR tests were ordered from July to December 2023. Seventy-five (67.6%) results did not affect patient management, 18 (16.2%) results affected patient management, and the treatment impact of 18 (16.2%) results is unknown because they were from outside consult cases. There were no instances in which antibiotic therapy was completely discontinued due to a negative broad range PCR result. Concurrent in-house microbiology testing yielded a positive result in 15 (13.5%) cases, of which 8 (53%) had a negative broad range PCR result and 2 (13.3%) had a conflicting broad range PCR result. Thirty-eight (34.2%) specimens were formalin fixed paraffin embedded tissue, 29 (26.1%) were fresh tissue, 13 (11.7%) were ESWABS, and the remaining 31 specimens were various fluid types (27.9%). While fresh tissue is the preferred specimen, broad range PCR detected an organism in 20 (53%) formalin fixed paraffin embedded tissue specimens, 11 (37.9%) fresh tissue specimens, 3 (23.1%) ESWAB specimens, and 2 (6.5%) fluid specimens (abscess aspirate and cerebrospinal fluid). Improvements in physician communication and laboratory workflow are necessary to improve the specimen quality and thus the utility of this referral test at our institution.

Detecting and Reporting Extended Spectrum Beta-Lactamases Producers: Evaluation of Three Approaches and the Clinical Impact

Abstract Introduction/Objective Since the COVID-19 pandemic, bacteria producing extended spectrum beta-lactamases (ESBLs) have increased >30%. Laboratories can perform phenotypic microbroth dilution or molecular approaches to identify ESBL producers. However, the gold standard is a laborious double disc synergy test. We evaluated the concordance among the three approaches, the clinical impact, and justification of reporting ESBL producers. Methods/Case Report Seventy-eight ESBL producers identified by microbroth dilution (MicroScan WalkAway, Beckman Coulter, Brea, California, USA) or detection of blaCTX-M gene from blood cultures (BCID2 Panel, BioFire, Biomerieux, Salt Lake City, Utah, USA) were tested using double disc synergy test retrospectively. Concordance among the methods evaluated. Discordant cases were reviewed with subsequent patient chart review. Results (if a Case Study enter NA) Tested isolates included E. coli (n=44, 57%), K. pneumoniae (n=19, 24%), K. oxytoca (n=7, 9%), and P. mirabilis (n=8, 10%). Concordance between microbroth dilution and disk diffusion was 86% (67/78). For isolates with genotypic testing (n=16), concordance with microbroth dilution and disk diffusion was 93% and 88%, respectively. Overall concordance was 88%. There were 12 isolates (E. coli:8, P. mirabilis: 2, and K. pneumoniae:2) with discordant results from one method. The susceptibility profile of discordant isolates revealed resistance to ceftriaxone or ceftazidime (11/12), penicillin (11/12), and aztreonam (6/12); 10/12 isolates were resistant to at least 2 groups of these antibiotics, a phenotype of ESBL producers. Clinical teams acknowledged presence of ESBLs in 83% (10/12) of cases and 58% (7/12) warranted treatment with meropenem or combinational therapy. Infection prevention implemented contact isolate procedures in all cases. Conclusion Our current in-house methods (e.g., microbroth dilution and genotypic testing) are still justified for ESBL testing to optimize patient care in a timely fashion. In the minor cases with discordant results, clinical care was unaffected. Laboratory workflow changes need to take laboratory efficiency, patient outcomes, and actionable clinical changes into consideration.

Hematology instruments don’t speak the same language: a comparison study between flagging messages of sysmex XN-1000 and alinity H

Abstract Objectives While manual review is the gold standard, automated hematology analyzers are increasingly used. This study assessed the efficiency of white blood cell (WBC)-related flagging messages from the Sysmex XN-1000 and Alinity hq analyzers compared to peripheral blood smear (PBS) findings and evaluated their inter-platform agreement. Methods K3EDTA blood samples from hospitalized patients were analyzed using the Sysmex XN-1000. Samples triggering a morphology flag were reanalyzed on the Alinity hq, with PBS reviewed per CLSI protocol H20-A2-2007. Results Of 5530 samples, 196 had morphology-related flags requiring PBS review. Sysmex flagged 144 samples with leukocyte-related messages; Alinity flagged 120. The positive predictive value (PPV) for the Left Shift flag was 100 % for Sysmex and 77.5 % for Alinity; for Immature Granulocytes, it was 19.4 % for Sysmex and 94.6 % for Alinity. The Blast Flag’s PPVs were 9.3 % for Sysmex and 17.9 % for Alinity. Left Shift specificities were high (>94 %), but sensitivities varied. Sysmex showed 100 % sensitivity for the Blast flag but moderate specificity (53 %), while Alinity performed well (77–82 %). Agreement between platforms ranged from poor to good. Conclusions Tailored SOPs are crucial for optimizing laboratory workflow based on different flagging performances. Understanding each analyzer’s strengths and limitations improves interpretation and workflow management.

Efficiently Improving Laboratory Workflow with Continuous Sample Loading by Validating the COBAS 5800 for HIV and HCV Viral Loads

Abstract Introduction/Objective A regional veteran affairs medical center (VAMC) was using the COBAS AmpliPrep/COBAS Taqman (Roche, Basel Switzerland) with a throughput of 72 tests/8 hours without continuous loading capability. However, a newer cobas 5800 System (Roche, Basel Switzerland) was validated to allow for continuous loading with better parameters for workflow including 144 tests/per 8 hours with a capacity for continuous loading of samples without batching. As validation experiences between the two instruments is sparse in the literature, the validation is described. Methods/Case Report The validation process included a linearity study using 24 samples with levels (100, 600, 6,000, 60,000, 600,000, 2,000,000, and 6,000,000 copies/mL for HIV and 100, 300, 3,000, 30,000, 300,000, 3,000,000, and 30,000,000 copies/mL for HCV) across the analytical range, a precision study at a low (1,000 copies/mL) and high (100,000 copies/mL for HIV, 1,000,000 copies/ML for HCV) values of a triplicate run over 5 days, an accuracy study based on the precision study, a limit of detection study using 20 control samples at the limit of detection, control monitoring (high and low positive controls) over 9 runs, and a method correlation between the Cobas 5800 and the Cobas AmpliPrep/COBAS Taqman. Results (if a Case Study enter NA) The validation study resulted as expected. For the method correlation, the results were plotted and evaluated with an R2 of 0.937 (HIV from 91 samples) and 0.9646 (HCV from 74 samples). Linearity across the analytical range had an R2 of 0.9967 (HIV) and 0.9950 (HCV). All samples were detected at the limit of detection study. Both the accuracy and precision yielded expected results. The values from running the controls (high and low positive) over 9 runs remained within the expected range and within two standard deviations for all runs. Conclusion The COBAS 5800, which has improved capabilities compared to the COBAS AmpliPrep/COBAS Taqman, was validated for clinical use successfully.

Performance of Gram Stain Characteristics for Predicting Culture Growth in Lower Respiratory Specimens Across Multiple Institutions

Abstract Data from Gram stains performed on clinical specimens can guide clinical decision-making and downstream laboratory workflows. However, the extent to which Gram stain results predict gold-standard culture results, and the generalizability of this performance across sites, warrants additional exploration. We sought to discover which Gram stain features would be associated with clinically significant culture growth (“growth”). To do so, 574 remnant specimens from the lower respiratory tract collected from four institutions were analyzed. A standardized Gram stain and culture protocol was performed across all study sites. Final reference organism identification was assigned using MALDI-ToF MS, and clinically significant growth was defined as any organism reported to the medical record. Gram stains with mixed microorganisms detected were considered concordant if ≥2 organisms of different Gram stain appearances were identified in culture. Growth was observed in 53% of specimens, including 25% of specimens in which Gram stain demonstrated no organisms. The 95% confidence intervals (CI) of the site-wise growth rates were 30-42%, 42-52%, 51-67%, and 60-77% (p < 0.001 by Chi-squared). By Gram stain morphology, 53-69% of specimens with Gram-positive cocci grew any clinically significant bacteria, while 31-49% grew a concordant Gram-positive cocci. 65-85% of specimens with Gram-negative bacilli grew any clinically significant bacteria, while 59-74% grew a concordant Gram-negative bacilli. 63-83% of specimens with mixed microorganisms grew 2 or more clinically relevant bacteria of differing Gram stain morphologies. Specimens from bronchoalveolar lavages (BALs) were less likely to have growth (30-42%) than endotracheal aspirates (66-77%). Polymorphonuclear leukocyte (PMNs) abundance was associated with culture growth, with Gram stains showing no, rare, few, moderate, or abundant PMNs demonstrating growth 28, 44, 52, 60, and 67% of the time (p < 0.001). Specimens with None and few squamous epithelial cells on Gram stain demonstrated growth 38-52% and 59-68% of the time (p < 0.001). No significant difference in growth was observed for red blood cells. Organism abundance on Gram stain was significantly associated with culture growth, with growth rate CIs being 20-32% for no organisms, 44-62% for rare, 58-77% for few, 70-93% for moderate, and 81-95% for abundant organisms seen. The extent to which these associations could guide the development of decision rules or machine learning models that demonstrate acceptable negative predictive value for pathogen growth to alleviate the operational burden of low-utility cultures is an exciting future direction to explore.

The Expression of miR-211-5p in Sentinel Lymph Node Metastases of Malignant Melanoma Is a Potential Marker for Poor Prognosis

Metastatic primary cutaneous melanoma is a frequently fatal disease despite recent therapeutic advances. Biomarkers to stratify patients’ prognosis are lacking. MicroRNAs (miRNAs) are small, non-coding RNAs. We aimed to determine the expression of miR-211-5p in primary tumors and metastases of malignant melanoma and its potential use as a prognostic biomarker. We performed in situ hybridization for miRNA-211-5p on 109 FFPE melanoma samples from 76 patients, including 31 paired primary tumor/metastasis samples. For validation, we performed in silico analyses of TCGA skin cutaneous melanoma (SKCM) cohort. High miR-211-5p expression was more frequent in primary tumors (70.8%) compared to metastases (39.3%). In metastases, it was associated with a significantly worse overall survival. Data from TCGA SKCM cohort confirmed that high miR-211-5p expression in melanoma metastases, but not primary tumors, is associated with worse overall survival. MiR-211-5p expression in metastases is associated with a shorter survival, emphasizing the potential of miR-211-5p as a risk predictor for a less favorable clinical outcome in metastatic disease. In situ hybridization could be implemented in a routine laboratory workflow and can be performed on diagnostic tissue.

A-205 Evaluating the Cost and Importance of Supply Chain Resilience in the Clinical Laboratory

Abstract Background Recent pandemics, epidemics and outbreaks continually underscore the critical importance of resilient supply chains in healthcare, particularly in clinical laboratories where timely access to supplies is essential for patient care. Supply chain disruptions, whether due to global crises or localized challenges, can significantly impact laboratory operations, leading to delayed diagnoses, compromised patient outcomes, and increased costs. It is estimated that 70%-80% of a patients’ EMR is clinical laboratory results. Despite this, supply chain resilience in clinical laboratories remains an under-addressed issue and remains a buzzword. Methods To evaluate the cost and importance of supply chain resilience in the clinical laboratory, we conducted a comprehensive review and interviews with 9 Healthcare Supply Chain experts analyzing the impact of supply chain disruptions on laboratory operations and patient care. Data was also collected from a diverse range of clinical laboratories, including hospitals, independent labs, and research institutions, spanning different geographic regions as well as a survey of 50 Laboratory experts with a 50% response rate. Key metrics assessed included: -Frequency and duration of supply chain disruptions. -Financial costs incurred due to disruptions, including expenses related to expedited shipping, alternative sourcing, and inventory management. -Impact on laboratory workflow, turnaround times, and patient care outcomes. -Strategies employed to mitigate supply chain risks and enhance resilience. Results Our review revealed findings regarding the cost and importance of supply chain resilience in the clinical laboratory: -Supply chain disruptions were frequent, with 85% of laboratories experiencing at least one significant disruption in the past year and 100% in experienced disruptions 2022. -The average duration of disruptions was 2-3 weeks, leading to substantial delays in test processing and patient care. -Financial costs associated with disruptions averaged $50,000 per laboratory per annum, including expenses for rush orders, and premium-priced alternatives. -Common strategies employed were increased inventory or safety stocks, multi-vendor sourcing, and supply chain mapping. Conclusions The findings of this study underscore the critical importance of supply chain resilience in the clinical laboratory. Supply chain disruptions are not just inconveniences; they pose significant risks to patient safety, operational efficiency, and financial sustainability. Investing in supply chain resilience is imperative for laboratories to fulfill their mission of delivering timely and accurate patient results. To continue to enhance supply chain resilience, laboratories must adopt a proactive approach, leveraging data-driven insights and collaborative partnerships. This includes diversifying supplier networks and fostering closer collaboration between laboratory and procurement teams.

A-138 Implications of native protein conformation in the IgM quantification: total Ig vs HLC methods comparison

Abstract Background For IgM monoclonal gammopathies such as Waldenström Macroglobulinemia, the diagnosis, risk stratification and monitoring response to therapy is based on the detection and quantification of the secreted IgM monoclonal protein. Accurate IgM measurement is challenging due to its complex nature and the occurrence in higher polymeric structures (i.e., pentamers or hexamers), as well as heterogeneity and inherent subjectivity of the selected common methodologies. The recently developed Heavy/Light chain assay (Binding Site, part of Thermofisher Scientific) allows the separate determination of the IgM-Kappa and IgM-Lambda molecules, offering an alternative method to the serum electrophoresis (SPE) with reported higher sensitivity (Ref. Boyle E. et al, Clin Cancer Research 2016). In this study we explore the effect of the molecular structure on 3 different analytical techniques for accurate IgM measurements Methods 214 serum samples from patients (age median 63yo) under follow-up at our hospital were tested for: IgG, IgA, and IgM levels (immunoturbidimetry, either on a Beckman Coulter AU5800 analyser; Nyon, Switzerland; or a Cobas c 702 system, Roche Diagnostics); Hevylite assay (on an Optilite, Binding Site); and SPE and Immunofixation (Capillarys 3 Octa and Hydrasys 2, Sebia Inc.). The effect of the molecular conformation was evaluated through sample depolymerization with N-Acetylcysteine (NAC) according to the manufacturer’s instruction (Sebia Inc.) and IgM quantification by: tIgM (immunoturbidimetric total Ig); red-Ig (idem after NAC reduction); and, HLC-Ig (i. e. sum of the IgM-K+IgM-L heavy/light chain pair measured by Hevylite (Binding Site)). Results Total-Ig, red-Ig, and HLC-Ig returned similar results for IgG and IgA immunoglobulins (Kruskal-Wallis test, p-value > 0.05), and Passing Bablok regression analysis showed good agreement between the three methods, except for higher IgA levels. In the later, both HLC-IgA levels red-IgA values were higher than total-IgA. Regarding the IgM, PB regression revealed a significant proportional bias, with obtained values approx. 2,5x higher by red-IgM and approx. 1,4x by HLC-IgM methods than tIgM (red-IgM=-5.5+2.42*tIgM, Spearman’s r=0.995; HLC-IgM=-0,77+1.34*tIgM, Spearman’s r=0.978; red-IgM=-6.29+1.82*HLC-IgM, Spearman’s r=0.98). So, both red-IgM and HLC-IgM results are higher than total IgM. Of note, 1 sample presented antigen excess, resulting in unusually low IgM levels by tIgM but high red-IgM and high HLC-IgM levels coherent with the patient’s clinical condition. 75 samples had monoclonal protein measurable by SPE, showing good correlation with the three methods, however with greater proportional errors between measurements with other techniques Conclusions IgM molecular conformational status may affect the epitopes exposed and, therefore, available for the different assays’ recognition. Higher IgM complexes depolymerization into monomeric conformation results in higher IgM levels, which agree better with the Hevylite than with the total IgM measured previous NAC reduction, reflecting the impact of the native protein conformation in the IgM precise detection. Although also affected by the conformational status, Hevylite IgM results were closer to the reduced IgM levels than the obtained by the total IgM assay, therefore offering a sensitive assay that does not need a reduction treatment for a more accurate IgM quantification, optimizing the laboratory workflow

A-162 Improved Laboratory Workflow using Automated Detection of Hemolysis, Icterus, and Lipemia for Coagulation Testing

Abstract Background Managing preanalytical variables is critical to providing quality laboratory test results. However, this can be a challenge for laboratory staff, particularly with manual detection of interfering substances and complicated workflows. For coagulation testing, we assess specimen integrity and acceptability by visual checks and quantification of interfering substance on a chemistry analyzer. To improve this subjective process, we evaluated the technical performance of a new model of coagulation analyzer with automated preanalytical specimen integrity detection. Our objective was to determine if we could reduce the number of specimens requiring visual inspection/off-analyzer interference testing in order to simplify our testing workflow. Methods Citrated plasma specimens received in the Hospital Clinical Laboratory at Mayo Clinic (Rochester, MN) were tested on the TOP ACL 500 or TOP ACL 550 Series Coagulation analyzers (Werfen, Boston, MA) according to manufacturer’s instruction. Specimens tested on the TOP 500 were visually inspected for hemolysis, icterus, and lipemia (HIL). If the technologist detected a possible interferent, an aliquot of plasma was analyzed on our cobas c501 chemistry analyzer (c501) (Roche Diagnostics, Indianapolis, IN) to obtain HIL values. Laboratory-established or manufacturer-defined interference thresholds were applied in determining specimen acceptability. For samples tested on the TOP 550, specimen integrity was assessed by the instrument’s automated interference detection module. The analyzer reported HIL as an “interference cloud” or estimated range, rather than a single value like the c501. HIL values were estimated by visual assessment of the low end of the “interference cloud”. Values were confirmed on the c501 only for specimens with an “interference cloud” at/exceeding the test-specific interference thresholds. We analyzed data from a 2-month period pre- (TOP 500) and post-implementation (TOP 550). The percent of specimens requiring quantitation/confirmation on the c501 was calculated. Statistical significance was calculated using the Chi-squared test where significance was defined as p<0.01. Correlation between c501 and TOP 550 estimated HIL values was evaluated. Results A total of 2.2% (171/7605) and 1.3% (113/8983) of specimens tested on the TOP 500 and TOP 550, respectively, required HIL measurements on the c501 (p<0.001). Of those samples, 8.2% (14/171) and 14.2% (16/113) from the TOP 500 and TOP 550, respectively, had HIL values above the interference thresholds and were rejected by the laboratory. Comparison of the estimated HIL values from the “interference cloud” and from the c501 resulted in slopes (Pearson correlation coefficients) of: H 1.56 (0.77), I 0.67 (0.97), and L 1.35 (0.99). Conclusions In comparison to our workflow with visual assessment of interference, use of the automated interference detection functionality on the TOP 550 instrument resulted in a lower percentage of specimens requiring HIL measurements on the chemistry analyzer. Agreement between interference measurements obtained on the c501 and the TOP 550 was moderate where TOP 550 overestimated the degree of hemolysis and lipemia and underestimated icterus. Implementation of automated interference detection on the TOP 550 analyzer improved our workflow by eliminating the need for tedious and subjective visual checks and reducing the percentage of specimens requiring additional HIL measurements.

Mass spectrometry-based proteomics for source-level attribution after DNA extraction

Biological traces recovered from crime scenes serve as vital evidence in forensic investigations. While DNA evidence is frequently used to address the sub-source level of the hierarchy of propositions, the biological source of the DNA can be highly probative at the source level. Current body fluid detection methods pose certain limitations, such as reports of false positive results from some of the presumptive and/or confirmatory tests in current use. These tests are also individual tests for the detection of one body fluid, meaning that if the sample is suspected to be a mixture of multiple body fluids, then different tests would need to be conducted to confirm the body fluid(s) present, which may exhaust small amounts of available biological trace. Proteomics applications for the identification of body fluids have been previously explored, and potential biomarkers indicative of body fluids discovered from liquid-chromatography tandem mass spectrometry (LC-MS/MS) methods have been reported. This work focuses on developing a mass spectrometry-based proteomics approach for the identification of body fluids by targeting discriminating peptide biomarkers from the non-DNA component left over after DNA extraction of samples. The non-DNA component is typically a waste product but with unappreciated evidential value. Our methodology for the purification of proteins from the post-DNA extraction waste includes an acetone precipitation and single-pot solid-phase-enhanced sample preparation (SP3) technique, microwave-assisted trypsin digestion, and LC-MS/MS analysis of the resultant peptides. Preliminary results from this proof-of-concept study include a list of potentially discriminating proteins and peptides for blood, saliva, and semen developed from the analysis of post-DNA extraction waste. Our method allows for multiple analytes to be targeted simultaneously from a DNA profiling waste stream and we anticipate that it could eventually be incorporated into standard forensic laboratory workflows.

A novel method for the simultaneous determination of drugs of abuse, ethyl glucuronide and synthetic opioids in human hair through a single digestion, purification and analysis in LC-MS/MS

Polydrug use is a serious health and social problem worldwide. Over the past several years, there has been an increasing tendency to combine narcotics, alcohol, sedatives, and/or stimulants. To the traditional drugs of abuse and alcohol, an increase of new abuse drugs such as synthetic opioids has been added. In the current study, the development and validation of an innovative and fast analytical procedure has been presented to determine drugs of abuse, ethyl glucuronide and synthetics opioids in 30 mg of human hair through a single digestion, purification and analysis in LC-MS/MS. A combine simple preparation of hair sample followed to a single chromatographic run of 10 min has been proposed. A full validation for 54 target analytes for the parameters of selectivity, linearity, limit of detection, limit of quantification, accuracy, precision, matrix effects, recovery, and dilution integrity was successful completed. The method was linear in different ranges with r values of at least 0.990; the value to the validated LLOQ values were in the range 0.1–100 pg/mg. The method offered satisfactory precisions (CV<15 % and accuracy ± 20 %). In conclusion, a significant reduction in the overall times of the analytical procedure and the reduction of consumables costs make this method extremely advantageous and undoubtedly useful in routine laboratory workflow analyses and open the way to the prospect of a further implementation which also includes other classes of xenobiotics.

Detection and differentiation of low virulence and virulent Orthoavulavirus javaense using a molecular beacon with RT-LAMP

Newcastle disease (ND), an economically important disease in poultry, is caused by virulent strains of the genetically diverse Orthoavulavirus javaense (OAVJ). Laboratories rely on quantitative real-time reverse transcription PCR (qRT-PCR) to detect OAVJ and differentiate between OAVJ pathotypes. This study demonstrates that a fusion cleavage site based molecular beacon with reverse transcription loop mediated isothermal amplification (MB-RT-LAMP) assay can detect and differentiate OAVJ pathotypes in a single assay. Data show that the assay can rapidly identify diverse OAVJ genotypes with sensitivity only one log-fold lower than the current fusion qRT-PCR assay (104 copies), exhibits a high degree of specificity for OAVJ, and the molecular beacon can differentiate mesogenic/velogenic sequences from lentogenic sequences. Further, data show that a two-minute rapid lysis protocol preceding MB-RT-LAMP can detect and differentiate OAVJ RNA from both spiked samples and oropharyngeal swabs without the need for RNA isolation. As the MB-RT-LAMP assay can rapidly detect and discriminate between lentogenic and mesogenic/velogenic sequences of OAVJ within one assay, without the need for RNA isolation, and is adaptable to existing veterinary diagnostic laboratory workflow without additional equipment, this assay could be a rapid primary screening tool before qRT-PCR based validation in resource limited settings.

Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories.

The emergence and re-emergence of arthropod-borne viruses is a public health threat. For routine surveillance in public health laboratories, cost-effective and reproducible methods are essential. In this review, we address the technical considerations of high-throughput sequencing methods (HTS) for arbovirus surveillance in national health laboratories, focusing on pre-sequencing, sequencing, and post-sequencing approaches, underlining the importance of robust wet and dry laboratory workflows for reproducible analysis. We aim to provide insights for researchers and clinicians interested in arbovirus, diagnosis, and surveillance by discussing current advances in sequencing methods and bioinformatics pipelines applied to arboviruses.

Towards robotic laboratory automation plug & play: Reference architecture model for robot integration

Supportive robotic solutions take over mundane, but essential tasks from human workforce in biomedical research and development laboratories. The newest technologies in collaborative and mobile robotics enable the utilization in the human-centered and low-structured environment. Their adaptability, however, is hindered by the additional complexity that they introduce. In our paper we aim to entangle the convoluted laboratory robot integration architectures. We begin by hierarchically decomposing the laboratory workflows, and mapping the activity representations to layers and components of the automation control architecture. We elaborate the framework in detail on the example of pick-and-place labware transportation - a crucial supportive step, which we identified as the number one area of interest among experts of the field. Our concept proposal serves as a reference architecture model, the key principles of which were used in reference implementations, and are in line with international standardization efforts.

Narrative review of latest research progress about robotic percutaneous coronary intervention.

Robotic percutaneous coronary intervention (R-PCI) is a novel technology in which operators can manipulate guidewires and catheter devices in interventional cardiology. This approach provides great benefits to interventional cardiologists in terms of reducing both radiation exposure and orthopedic injuries. Several large, high-quality cohort studies have confirmed the short-term safety and high technical success rate of R-PCI. However, randomized long-term data are still needed before adopting them as part of standard coronary interventions. Furthermore, tele-stenting for complex coronary lesions has significant potential for R-PCI. We need to overcome the present relevant challenges for its application such as inherent delays, bedside care for unstable patients from R-PCIs to manual PCIs (M-PCIs), incompatibility for a thrombus aspiration catheter and heavily calcified lesions. There is a great future in laboratory workflow teams, 3D-printed anatomical models and multiple joint collaborative control algorithms. This narrative review summarizes the latest developments in R-PCI, with a focus on developments in robotic technology, and discusses the current and future potential use of R-PCI in clinical practice globally.

Reflex Xpert MTB/XDR Testing of Residual Rifampicin-Resistant Specimens: A Clinical Laboratory-Based Diagnostic Accuracy and Feasibility Study in South Africa.

The World Health Organization-approved Xpert MTB/XDR test detects Mycobacterium tuberculosis and resistance to isoniazid, fluoroquinolones, ethionamide, and injectable drugs directly in specimens. This pragmatic, laboratory-based study assessed the diagnostic accuracy and feasibility of a reflex testing approach, where Xpert MTB/XDR was performed on residual specimens previously processed for Xpert MTB/RIF Ultra. Routine respiratory specimens, processed for Xpert MTB/RIF Ultra, were stored in sample reagent buffer at 2°C-8°C. If rifampicin resistant, the residual specimen was assessed for adequate volume (≥2 mL) and tested with Xpert MTB/XDR, with storage time recorded. A second specimen was used for routine and reference standard testing (culture and sequencing). Specimens (99% sputum) from 763 participants submitted to 2 large routine laboratories were included. Xpert MTB/XDR yielded valid resistance detection results in 639 (84%), compared with 507 (66%) for routine testing (difference [95% CI], 18% [13%-22%]). The median turnaround time for results was 23 hours for Xpert MTB/XDR and 15 days for routine testing. While 748 specimens (98%) were ≥2 mL, only 102 (13%) were stored for ≤4 hours. By the reference standard, 284 of 394 (72%) were isoniazid resistant, and 57 of 380 (15%) were fluroquinolone resistant. The sensitivities of Xpert MTB/XDR were 94% (95% CI, 91%-97%) for isoniazid and 91% (81%-97%) for fluoroquinolone resistance detection. The specificities were 98% (94%-100%) and 100% (98%-100%), respectively. Xpert MTB/XDR performed favorably compared with the reference, and the reflex testing approach increased results availability over routine testing, while dramatically decreasing turnaround time from weeks to hours. Laboratory workflow precluded testing within the manufacturer-recommended 4-hour storage time, but longer storage did not appear detrimental.

Implementing an integrated molecular classification for gastric cancer from endoscopic biopsies using on-slide tests.

The availability of more effective biological therapy can improve outcomes of gastric cancer (GC), but most patients do not have access to personalized treatment. GC molecular classification helps identify patients suitable for specific therapies and provides useful prognostic information. To date, only a small number of patients have access to molecular classification. We proposed a working molecular classification that can be delivered using on-slide tests available in most histopathology laboratories. We used eight on-slide tests [in situ hybridization (ISH) for Epstein-Barr virus-encoded small ribonucleic acid (EBER) and immunohistochemistry (IHC) for MutL homolog 1 (MLH1), PMS1 homolog 2 (PMS2), MutS homolog 2 (MSH2), MutS homolog 6 (MSH6), E-cadherin, β-catenin and p53] to classify GC into one of six categories: GC associated with Epstein-Barr virus (GC-EBV), GC mismatch repair deficient (GC-dMMR), GC with epithelial-mesenchymal transition (GC-EMT), GC with chromosomal instability (GC-CIN), GC genomically stable (GC-GS) and GC not otherwise specified (GC-NOS)∕indeterminate. The classification has provision also for current and future on-slide companion diagnostic (CDx) tests necessary to select specific biological therapies and, as proof of principle, in this study we used three CDx tests currently required for the management of GC [human epidermal growth factor receptor 2 (Her2), programmed cell death-ligand 1 (PD-L1) 22C3 and Claudin18.2 (CLDN18.2)]. This paper describes the necessary tissue pathways and laboratory workflow and assesses the feasibility of using this classification prospectively on small endoscopic biopsies of gastric and gastroesophageal junction adenocarcinoma. This work demonstrates that such molecular classification can be implemented in the context of a histopathology diagnostic routine with little impact on turnaround times and laboratory capacity. The widespread adoption of a molecular classification for GC will help refine prognosis and guide the choice of more appropriate biological therapy for these patients.

The Milan system atypia of undetermined significance: 5-year performance data.

The objective of this study was to evaluate the diagnostic performance of the category atypia of undetermined significance (AUS) at the authors' institution based on the Milan System for Reporting Salivary Gland Cytopathology. All AUS cases diagnosed at Fimlab Laboratories between January 1, 2018, and December 31, 2022, were included. Histologic verifications were checked until May 31, 2023. The upper-bound and lower-bound risk of malignancy and risk of neoplasm were calculated. The timelines between the pathology laboratory workflow and patient management were also calculated. From 1157 fine-needle aspirations (FNAs), 162 (14.0%) AUS cases were diagnosed in 146 patients, with an average±standard deviation age of 66.1±14.9 years. There was variation in the AUS percentages, with higher values during the coronavirus disease 2019 pandemic years (15% and 17.5% in 2020 and 2021, respectively). Seventy-five cases (46.3%) had histologic follow-up: 16 were malignant neoplasms, and 36 were benign neoplasms. The upper and the lower bounds of the-risk of malignancy and risk of neoplasm were 21.3% and 69.3% and 9.9% and 32.1%, respectively. The average time from the first FNA with an AUS diagnosis to surgical resection ranged from 6 to 682 days, and the time to the first repeat FNA ranged from 10 to 691 days. The results indicated higher percentages of AUS cases compared with the reference value, which may be attributed to the impact of the coronavirus disease 2019 pandemic. The risk of malignancy calculated in this study was closer to the reference value from the first edition of the Milan System for Reporting Salivary Gland Cytopathology compared with the second edition.