Sample Turnaround Time Research Articles

Effect of Pre-Analytical Line Settings on Artefactually Elevated Anion Gap Results

Abstract Introduction When the core lab at a large tertiary care hospital introduced an automated laboratory system from a major manufacturer, the automated line aliquoted patient serum into open cups for all chemistry testing. It was subsequently discovered that if sample testing was delayed, electrolyte abnormalities could be introduced from evaporation, resulting in an increased anion gap (presumably due to a loss of bicarbonate with evaporation of carbon dioxide). To address this issue, the core lab changed the sample processing protocol in April 2023 from an open cup system to testing primary tubes on the analyzers. The purpose of this study was to evaluate the impact of switching to a primary tube testing system on artefactually elevated anion gap results. Methods Equivalent ten-week blocks of anion gap, creatinine and sample turnaround time (from receipt on the line to analyzer perform time) results from pre- to post-primary tube conversion were collected from the laboratory information system. Data from weekend testing and from repeat samples from the same patient were excluded. Data was cleaned and analyzed using R. Results Multivariable linear regression showed that when adjusted for the turnaround time and creatinine result, the open cup system was significantly associated (p<0.0001) with a 0.95 [95% CI 0.69-1.21] increase in anion gap. There was a positive relationship between turnaround time and anion gap, with a slope of 0.017 (i.e., a 0.017 increase in anion gap per minute delay; p<0.0001). Overall, the proportion of abnormal results (defined as anion gap >=16) decreased from 26% to 10% after switching to a primary tube testing system. Furthermore, there was an association between the times of day in which the lines were overloaded with specimens, turnaround time, and an increase in abnormal anion gap results. Overall, the mean anion gap decreased by 1 with a turnaround time of one hour and 2 after two hours by switching to the primary tube system. This trend in anion gap was largely driven by a corresponding decrease in bicarbonate. Sodium and chloride levels did not show any relationship with turnaround time. Conclusions Using an open cup system for electrolyte testing can cause spuriously elevated anion gap levels, especially with testing delays. Switching to a primary tube testing system largely resolved the issue; however, the data still showed a weakly positive relationship between turnaround time and anion gap for the primary tube testing system, so additional work is needed to identify potential causes of this relationship.

Direct analysis in real time mass spectrometry (DART-MS/MS) for rapid urine opioid detection in a clinical setting

Background and aimsCurrent laboratory methods for opioid detection involve an initial screening with immunoassays which offers efficient but non-specific results and a subsequent liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmation which offers accurate results but requires extensive sample preparation and turnaround time. Direct Analysis in Real Time (DART) tandem mass spectrometry is evaluated as an alternative approach for accurate opioid detection with efficient sample preparation and turnaround time. Materials and methodsDART-MS/MS was optimized by testing the method with varying temperatures, operation modes, extraction methods, hydrolysis times, and vortex times. The method was evaluated for 12 opioids by testing the analytical measurement range, percent carryover, precision studies, stability, and method-to-method comparison with LC-MS/MS. ResultsDART-MS/MS shows high sensitivity and specificity for the detection of 6-acetylmorphine, codeine, hydromorphone, oxymorphone, hydrocodone, naloxone, buprenorphine, norfentanyl, and fentanyl in urine samples. However, its performance was suboptimal for norbuprenorphine, morphine and oxycodone. ConclusionIn this proof-of-concept study, DART-MS/MS is evaluated for its rapid quantitative definitive testing of opioids drugs in urine. Further research is needed to expand its application to other areas of drug testing.

Lactate Dehydrogenase (LDH) audit report on the turnaround time of samples

Lactate Dehydrogenase (LDH) audit report on the turnaround time of samples

Comparison of the speed and quality of innovative and traditional pneumatic tube system transport outside of an emergency laboratory

BackgroundEnsuring the rapidity and accuracy of emergency laboratory test results is especially important to save the lives of patients with acute and critical conditions. To better meet the needs of clinicians and patients, detection efficiency can be improved by reducing extra-laboratory sample turnaround times (TATs) through the use of innovative pneumatic tube system (PTS) transport for sample transport. However, concerns remain regarding the potential compromise of sample quality during PTS transit relative to that occurring with manual transportation. This study was performed to evaluate the efficacy of an innovative PTS (Tempus600 PTS) relative to a traditional PTS in terms of sample transit time, sample quality, and the concordance of analytical results with those obtained from manually transported samples. MethodsIn total, 30 healthy volunteers aged >18 years were recruited for this study, conducted for five consecutive days. Venous blood samples were collected from six volunteers per day at fixed timepoints. From each volunteer, nine blood samples were collected into tubes with tripotassium ethylene diamine tetraacetic acid anticoagulant, tubes with 3.2 % sodium citrate, and serum tubes with separation gel (n = 3 each) and subjected to all tests conducted in the emergency laboratory in our hospital. 270 blood samples from 30 healthy volunteers were transported and analyzed, yielding 6300 test results. The blood samples were divided randomly into three groups (each containing one tube of each type) and transported to the emergency laboratory manually and with Tempus600 PTS and conventional Swisslog PTS, respectively. The extra-laboratory TATs, sample quality, and test results of the transported blood samples were compared. ResultsThe sample quality and test results did not differ according to the delivery method. The TAT was much shorter with the Tempus600 than with the other two transport modes (58.40 ± 1.52 s vs. 1711.20 ± 77.56 s for manual delivery and 146.60 ± 1.82 s for the Swisslog PTS; P = 0.002). ConclusionBlood sample transport with the Tempus600 PTS significantly reduced the extra-laboratory TAT without compromising sample quality or test result accuracy, thereby improving the efficiency of sample analysis and the services provided to clinicians and patients.

Abstract 341: Co-detection of BCR::ABL1 common and atypical fusion and mutation using a novel NGS assay, Dup-Seq BCR-ABL1

Abstract The clinical management of CML and Ph+ ALL patients requires the identification of BCR::ABL1 transcript variants and drug resistance mutations. Currently these assessments need to be performed using separate assays resulting in higher sample requirements, longer turnaround times and higher costs. In this study a custom NGS assay (Dup-Seq BCR-ABL1) was developed and validated that enables co-detection and identification of transcript variants (common and atypical) and resistance mutations. The assay design covers BCR exon 1 to ABL1 exon 10 and employs duplicate PCR amplification of BCR-ABL1 from a single source of the 1st strand cDNA initiated by ABL1 specific priming. The custom data analysis pipeline enables overlapped mutation calling from duplicates as well as transcript determination. The assay minimizes the low-level artifacts that can be seen with other NGS-based BCR::ABL1 assays. This study demonstrates that the Dup-Seq BCR-ABL1 assay achieves high accuracy (PPA for fusion: 0.985; PPA and NPA for mutation at 0.978 and 0.9999, respectively) and sensitivity (LoD for mutation detection at 3% from 10,000 copies of BCR-ABL1 input). The use of the Dup-Seq BCR-ABL1 assay for both transcript variant identification and mutation detection provides comprehensive and accurate results for the clinical management of CML and Ph+ ALL patients while reducing sample requirements, testing costs and turnaround time. Citation Format: Jin Li, Zhenyu Yan, Lin Shi, Wei Li, Weihua Liu, Cynthia Spittle, Chad Galderisi. Co-detection of BCR::ABL1 common and atypical fusion and mutation using a novel NGS assay, Dup-Seq BCR-ABL1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 341.

Optimizing the Integration of Genetic Testing in AML Care in Community Practice: Insights from a Quality Improvement Initiative

Background The treatment landscape for acute myeloid leukemia (AML) is rapidly evolving, and with many of the more recently FDA approved treatments being targeted therapies, timely and actionable molecular and cytogenetic testing is critical to the management of AML patients. However, many challenges and barriers to optimal testing workflows impede clinicians' ability to integrate genetic testing in treatment decision-making. To improve quality care related to genetic testing in AML, we conducted a quality improvement (QI) study focused on evidence-based integration of genetic testing into routine practice for AML patients in community oncology clinics. Methods This QI initiative is comprised of baseline (N = 72) and follow-up provider surveys, and pre- and post-surveys of providers participating in small-group, team-based audit-feedback (AF) sessions across 5 community clinics. Survey questions were designed to assess knowledge, confidence, and experiences with genetic testing in AML. Care teams from each clinic, along with an expert AML oncologist and a hematopathologist, participated in AF sessions to (a) assess system-specific practice gaps identified via the provider surveys, (b) prioritize areas for improvement, and (c) develop action plans for addressing root causes. Results Provider Surveys: Providers top reported challenges encountered with integrating genetic testing into routine practice include determining whether to begin treatment prior to receipt of genetic testing result (56%)and applying genetic testing results to treatment decision-making (29%). For patients with AML, 70% of providers stated they were likely to start treatment prior to receiving testing results. When asked to report routine molecular testing practice patterns, 72% of providers reported testing for FLT3 mutations, 62% for IDH1/2 mutations, 65% for TP53 mutations, and 63% for NPM1 mutations; with further suboptimal reported practices in the use of NGS panels (58%; average turnaround time 15 days) and PCR (52%; average turnaround time 8 days). Overall, providers reported a 56% satisfaction rate with the processes implemented in the clinic related to sample preparation, timely review, and turnaround time of molecular diagnostics testing reports. AF Sessions: Providers participating in the AF sessions also reported determining whether to begin treatment prior to receipt of molecular testing results, long turnaround times and deciding on the appropriate molecular tests as top barriers to integrating testing in routine AML care. Clinicians reported improvements in high/very high confidence in their ability to select appropriate genetic tests to order for patients with AML (35% to 50%) and select targeted therapies based on genetic test results for AML patients (34% to 59%). Care teams set goals to improve turnaround times and testing workflows with pathology partners, as well as to maximize opportunities for patients to receive AML therapies for their specific mutation profile. Action plans to achieve these goals include improve team skills in choosing guideline-based genetic testing methods and targeted therapies and collaborate among clinical teams to improve ordering workflow and diagnostic sample preparation for genetic testing. Follow-Up Surveys: In 90-day follow up surveys, 100% of clinic champions reported upshifts in patients with targetable driver mutations receiving guideline-recommended treatment based on genetic testing results, and 4/5 clinics reported improved selection of guideline-recommended genetic testing prior to treatment initiation for AML patients. Conclusions Through this QI initiative, clinical teams identified barriers to integrating genetic testing into routine AML care, creating and implementing action plans to optimize genetic testing workflows and guideline-recommended targeted therapy selection. While meaningful confidence and action plan gains were demonstrated, these data underscore clinical practice gaps to address in future initiatives to support the integration of evidence-based genetic testing into AML care, including integrated education sessions with clinicians and pathologists. Study Sponsor Statement The study reported in this abstract was funded by independent educational grants from AbbVie, Inc. and Astellas Pharma Global Development, Inc., who had no role in the study design, execution, analysis, or reporting.

Development of a mobile laboratory system in hydrogen fuel cell buses and evaluation of the performance for COVID-19 RT-PCR testing

We designed and developed two new types of hydrogen fuel cell (HFC) buses (motorcoach and minibus) with a mobile laboratory system. Feasibility studies have been performed for mobile laboratory testing, particularly for the laboratory performance of COVID-19 RT-PCR (PCR). We evaluated the driving range capability, PCR sample size capacity, turnaround time (TAT), and analytical performance for the detection of SARS-CoV-2. Saliva samples were used for the current study, and the analytical performance was compared with that of the reference PCR. The estimated driving range and sample size capacity of the HFC and HFC minibus were 432 km and 2847 samples, respectively, for the HFC motorcoach and 313 km and 1949 samples for the HFC minibus. For the TAT, the median time between sample submission and completion of PCR was 86 min for the motorcoach and 76 min for the minibus, and the median time between sample submission and electronic reporting of the result to each visitor was 182 min for the motorcoach and 194 min for the minibus. A secondary analysis of 1574 HFC mobile laboratory testing samples was conducted, and all negative samples were found to be negative by reference PCR. Furthermore, all samples were confirmed to be positive by reference PCR or other molecular examinations.

A grain-by-grain comparison of apatite fission-track analysis by LA-ICP-MS and the External Detector Method

Laser-ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is increasingly used in fission-track analysis to determine the uranium content of host mineral specimens, particularly apatite. Fission-track dating by LA-ICP-MS (LAFT) has several advantages over the conventional External Detector Method (EDM), particularly in terms of sample turn-around times and the fact that neutron irradiations and the handling of radioactive materials are no longer necessary, while providing a similar level of in-situ information about parent nuclide (238U) concentrations. In addition, it facilitates the simultaneous measurement of multiple isotopes for double or triple-dating approaches or compositional characterisation. While it is often implicitly assumed that the EDM and LAFT fission-track dating approaches produce equivalent results, this assertion has yet to be adequately tested. We present an extensive dataset of apatite fission track results from 17 samples representing a large range of fission-track ages (∼0–2 Ga), 238U concentrations (0.14–410 ppm) and thermal histories that were analysed grain-by-grain using both techniques in order to investigate whether they yield concordant results during routine fission-track analysis.Apart from a few outliers, our data show that 238U concentrations measured by the EDM and LAFT techniques yield indistinguishable results across at least three orders of magnitude when a similar calibration system against rapidly cooled standards (e.g., Durango) is used. Comparison of single grain pooled and central ages reveals that LAFT ages are within error of EDM ages for apatite fission track standards such as Fish Canyon Tuff or Durango, as well as for a range of other samples whose shorter mean confined track lengths (<13 μm) and broader track distributions indicate they experienced more complex cooling histories. The most important conclusion here is that both the conventional EDM and LAFT methods can be expected to yield identical results for the breadth of ages, 238U concentrations, and underlying thermal histories commonly found in real world apatites.Importantly, the aggregate empirical calibrations for EDM and LAFT mask an underlying assumption that the mean etchable range of fission fragments is a constant having the mean value observed for spontaneous tracks in age standards such as the Durango apatite. Given that this assumption is known to be false in the great majority of samples, it is our view that empirically derived EDM and LAFT fission-track ages are best considered as model ages and that there should be greater clarity about the assumptions involved in their calculation.

Laboratory Automation in Microbiology: Impact on Turnaround Time of Microbiological Samples in COVID Time.

Laboratory Automation (LA) is an innovative technology that is currently available for microbiology laboratories. LA can be a game changer by revolutionizing laboratory workflows through efficiency improvement and is also effective in the organization and standardization of procedures, enabling staff requalification. It can provide an important return on investment (time spent redefining the workflow as well as direct costs of instrumentation) in the medium to long term. Here, we present our experience with the WASPLab® system introduced in our lab during the COVID-19 pandemic. We evaluated the impact due to the system by comparing the TAT recorded on our samples before, during, and after LA introduction (from 2019 to 2021). We focused our attention on blood cultures (BCs) and biological fluid samples (BLs). TAT recorded over time showed a significant decrease: from 97 h to 53.5 h (Δ43.5 h) for BCs and from 73 h to 58 h (Δ20 h) for BLs. Despite the introduction of the WASPLab® system, we have not been able to reduce the number of technical personnel units dedicated to the microbiology lab, but WASPLab® has allowed us to direct some of the staff resources toward other laboratory activities, including those required by the pandemic. LA can significantly enhance laboratory performance and, due to the significant reduction in reporting time, can have an effective impact on clinical choices and therefore on patient outcomes. Therefore, the initial costs of LA adoption must be considered worthwhile.

Clinical application value of Abbott Alinity analyzer in syphilis-specific antibody testing

Abstract Background: We aimed to investigate the clinical application value of Abbott Alinity analyzer in syphilis-specific antibody testing. Methods: A total of 100 patients admitted from June 2021 to June 2022 for early syphilis diagnosis were selected and subjected to Treponema pallidum (TP) antibody testing by chemiluminescent microparticle immunoassay (CMIA) using Abbott Alinity analyzer. With TP particle agglutination (TPPA) retesting as the gold standard for syphilis diagnosis, the signal-to-cutoff (S/CO) ratio of the TP antibody testing was plotted into the receiver operating characteristic curve to determine the diagnostic value of CMIA and CLIA in detecting positive TP antibody and to identify the optimal cutoff point. Results: In the case of S/CO ratio ≥7.00, the patients with positive CMIA were diagnosed with positive findings after TPPA confirmation. With the S/CO ratio of 1.00-4.99, the coincidence rate of CLIA with positive TPPA was 81.82% (45/55), and all patients with positive CLIA had positive results confirmed by TPPA test when the S/CO ratio was &gt;5.00. When the optimal cutoff value of S/CO ratio for TP was determined as 6.98 by CMIA, the sensitivity, specificity, and maximum area under the curve (AUC) were 94%, 88% and 0.91, respectively. At the optimal cutoff value (S/CO ratio: 4.56) determined by CLIA, the sensitivity was 84%, the specificity was 80%, and the maximum AUC was 0.84. Conclusions: In the case of S/CO ratio ≥7.00, both methods have high sensitivity and specificity, which can directly give positive reports and shorten the sample turnaround time.

The Effect of Total Laboratory Automation on Urine Culture Result Times in a Consolidated Laboratory.

The Provincial Health Directorate of Istanbul province (Turkey) established a consolidated laboratory network consisting of four regional central laboratories to reduce general laboratory costs and increase laboratory efficiency and quality in all affiliated hospitals. As part of the consolidation project, the Total Laboratory Automation (TLA) system was installed in the microbiology department of the ISLAB-2 central laboratory. In this study, the turnaround time (TAT) of urine samples of a satellite laboratory where the system was not installed and the ISLAB-2 central laboratory were compared to evaluate the effect of consolidation and the TLA. The TAT values of all urine samples processed between March 2021, when the TLA was installed, and October 2021, were retrospectively examined in the laboratory information system. While the TLA was used for the processing and evaluation of samples in the ISLAB-2 central laboratory, manual methods were employed in the satellite laboratory. Both laboratories used MALDI-TOF MS (bioMérieux, France) for bacterial identification and VITEK 2 Compact (bioMérieux, France) for antibiotic sensitivity testing. Kruskal-Wallis test was used to compare TAT between the two laboratories. p < 0.05 was taken as the level of statistical significance. A total of 78,592 urine cultures (71,906 in the central laboratory and 6,686 in the satellite laboratory) were included in the study. Negative samples were reported in 23.5 hours in the central laboratory and 37.1 hours in the satellite laboratory and positive samples in 55 hours and 61.7 hours in the same laboratories, respectively. The mean TAT of both positive and negative urine cultures were found statistically significantly lower in the central laboratory than in the satellite laboratory (p < 0.0001). While 82% of negative urine cultures were completed within the first 24 hours in the central laboratory, only 17% were processed in the satellite laboratory. While 61% of positive samples were processed within the first 48 hours in the central laboratory, 38% were completed in the satellite laboratory. We assume that TLA has a positive effect on the diagnosis and treatment of patients, thanks to its contribution to standardization, efficiency, increased quality, and earlier reporting.

Performance evaluation of the high sensitive troponin I assay on the Atellica IM analyser.

IntroductionThe Fourth Universal Definition of Myocardial Infarction Global Taskforce recommends the use of high sensitive troponin (hs-Tn) assays in the diagnosis of acute myocardial infarction. We evaluated the analytical performance of the Atellica IM High-sensitivity Troponin I Assay (hs-TnI) (Siemens Healthcare Diagnostics Inc., Tarrytown, USA) and compared its performance to other hs-TnI assays (Siemens Advia Centaur, Dimension Vista, Dimension EXL, and Abbott Architect (Wiesbaden, Germany)) at one or more sites across Europe.Materials and methodsPrecision, detection limit, linearity, method comparison, and interference studies were performed according to Clinical and Laboratory Standards Institute protocols. Values in 40 healthy individuals were compared to the manufacturer’s cut-offs. Sample turnaround time (TAT) was examined.ResultsImprecision repeatability CVs were 1.1–4.7% and within-lab imprecision were 1.8–7.6% (10.0–25,000 ng/L). The limit of blank (LoB), detection (LoD), and quantitation (LoQ) aligned with the manufacturer’s values of 0.5 ng/L, 1.6 ng/L, and 2.5 ng/L, respectively. Passing-Bablok regression demonstrated good correlations between Atellica IM analyser with other systems; some minor deviations were observed. All results in healthy volunteers fell below the 99th percentile URL, and greater than 50% of each sex demonstrated values above the LoD. No interference was observed for biotin (≤ 1500 µg/L), but a slight bias at 5.0 g/L haemoglobin and 50 ng/L Tn was observed. TAT from was fast (mean time = 10.9 minutes) and reproducible (6%CV).ConclusionsReal-world analytical and TAT performance of the hs-TnI assay on the Atellica IM analyser make this assay fit for routine use in clinical laboratories.

Monitoring SARS-CoV-2 RNA in Wastewater with RT-qPCR and Chip-Based RT-dPCR: Sewershed-Level Trends and Relationships to COVID-19.

We evaluated the performance of reverse transcription quantitative PCR (uniplex and duplex RT-qPCR) and chip-based digital PCR (duplex RT-dPCR) using CDC N1 and CDC N2 assays for longitudinal monitoring of SARS-CoV-2 RNA in influent wastewater samples (n = 281) from three wastewater plants in Ohio from January 2021 to January 2022. Human fecal virus (PMMoV) and wastewater flow rate were used to normalize SARS-CoV-2 concentrations. SARS-CoV-2 measurements and COVID-19 cases were strongly correlated, but normalization effects on correlations varied between sewersheds. SARS-CoV-2 measurements by RT-qPCR were strongly correlated with 7-day moving average COVID-19 cases (average Spearman’s ρ = 0.58, p < 0.05). SARS-CoV-2 was detected more frequently in samples with duplex RT-dPCR than with duplex RT-qPCR during periods of low COVID-19 cases. Duplex and uniplex RT-qPCR N1 concentrations were more strongly correlated with cases (ρ = 0.62) than N2 (ρ = 0.52). RT-dPCR correlations (average ρ = 0.21) were weaker than those of RT-qPCR (average ρ = 0.58). We also share practical experience from establishing wastewater surveillance. Per sample, RT-qPCR had a lower cost ($6 vs $18) and sample turnaround time (3–4 h vs 7–9 h) than RT-dPCR. These findings reinforce selection and use of PCR-based wastewater surveillance tools.

Development of a rapid technique for sequential separation of plutonium/americium in nasal swab using solvent extraction and liquid scintillation spectrometry

A rapid radiochemical method has been developed for estimation of plutonium and americium in nasal swab using extractive liquid scintillation spectrometry. The method involves solvent extraction of plutonium and americium from pre-treated nasal swab using 0.2 M Di-(2-ethylhexyl)phosphoricacid prepared in toluene scintillator & back extraction of americium in aqueous phase using 0.35 M HNO3. Activity assessment was carried out using liquid scintillation spectrometry. Overall recovery obtained was 96% for plutonium and 76% for americium with a sample turnaround time of 3 h.

Multiplexed host immune response biosensor for rapid sepsis stratification and endotyping at point-of-care

Disease progression of sepsis has been perceived as a multifaceted phenomenon, considering the temporal host inflammatory response within individuals which requires early diagnosis. Herein, we present a multicohort analysis through temporal inflammatory biomarker profiling using Direct Electrochemical Technique Targeting (DETecT) sepsis device that measures and quantify cytokines (IL-6, IL-8, IL-10), chemokines (TRAIL, IP-10), and well-established inflammatory biomarkers (PCT, CRP) with a sample turnaround time of <5 min in small volume (<40 μL) patient plasma samples. The DETecT device positively correlated (r > 0.97) with the Luminex reference standard during clinical evaluation for a total of 124 sepsis patient samples. Low mean bias for all the biomarkers in Bland- Altman analysis indicated good agreement between the standard LUMINEX method and the developed DETecT sepsis device. We used the combinatorial power of rapidly measuring a panel of seven biomarkers, paired with a machine learning model, to effectively predict the patient outcomes when given two-time points in the early stages of sepsis. The device could predict patient mortality and recovery with over 92% accuracy by applying decision tree analysis. We envision this work would facilitate personalized treatment based on biomarker stratification to represent exactly where the patient belongs within the sepsis continuum. Measurable empirical data with a fast turnaround time would facilitate the DETecT sepsis device as a potential enabling technology that can play a crucial role in understanding sepsis prognosis and be leveraged for personalized therapeutics anywhere.

Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison.

Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was nonsignificant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.

Evaluation of the Speed, Accuracy and Precision of the QuickMIC Rapid Antibiotic Susceptibility Testing Assay With Gram-Negative Bacteria in a Clinical Setting.

The rapidly changing landscape of antimicrobial resistance poses a challenge for empirical antibiotic therapy in severely ill patients and highlights the need for fast antibiotic susceptibility diagnostics to guide treatment. Traditional methods for antibiotic susceptibility testing (AST) of bacteria such as broth microdilution (BMD) or the disc diffusion method (DDM) are comparatively slow and show high variability. Rapid AST methods under development often trade speed for resolution, sometimes only measuring responses at a single antibiotic concentration. QuickMIC is a recently developed lab-on-a-chip system for rapid AST. Here we evaluate the performance of the QuickMIC method with regard to speed, precision and accuracy in comparison to traditional diagnostic methods. 151 blood cultures of clinical Gram-negative isolates with a high frequency of drug resistance were tested using the QuickMIC system and compared with BMD for 12 antibiotics. To investigate sample turnaround time and method functionality in a clinical setting, another 41 clinical blood culture samples were acquired from the Uppsala University Hospital and analyzed on site in the clinical laboratory with the QuickMIC system, and compared with DDM for 8 antibiotics routinely used in the clinical laboratory. The overall essential agreement between MIC values obtained by QuickMIC and BMD was 83.4%, with an average time to result of 3 h 2 min (SD: 24.8 min) for the QuickMIC method. For the clinical dataset, the categorical agreement between QuickMIC and DDM was 96.8%, whereas essential and categorical agreement against BMD was 91.0% and 96.7%, respectively, and the total turnaround time as compared to routine diagnostics was shown to be reduced by 40% (33 h vs. 55 h). Interexperiment variability was low (average SD: 44.6% from target MIC) compared to the acceptable standard of ±1 log2 unit (i.e. -50% to +100% deviation from target MIC) in BMD. We conclude that the QuickMIC method can provide rapid and accurate AST, and may be especially valuable in settings with high resistance rates, and for antibiotics where wildtype and antibiotic-resistant bacteria have MIC distributions that are close or overlapping.

Separation optimization and quantitative analysis of phytoestrogens employing reverse-phase high-performance liquid chromatography with UV-VIS detection

The effect of different acidic modifiers on the separation of seven selected phytoestrogens by reverse-phase high-performance liquid chromatography has been described. Variation in the hydrocarbon chain length of organic acids as represented by acetic acid, propanoic acid, iso-butyric acid, and n-butyric acid as additives to the mobile phase had minimal effect on the separation of phytoestrogens but notably reduced sample turnaround times relative to the turnaround time linked with formic acid. Two different C18 columns were evaluated in attempts of optimize the phytoestrogen separations. Formic acid as a modifier in the mobile phase and an Atlantis C18 column provided the best overall separation at optimum gradient conditions. A higher acid concentration in the mobile phase did not improve the phytoestrogen separation. Higher column temperature (40 °C) provided an improved separation. Finally, the optimized method was used to quantify different phytoestrogens in selected different botanical samples. For this purpose, both internal and external standard methods were compared to obtain the quantitative results.

Performance evaluation of the fully automated random-access multiparameter SysmexCN-6000 hemostasis analyzer at a core laboratory with a high sample throughput.

We aimed to evaluate the performance of the fully automated multiparameter CN-6000 hemostasis analyzer. Performance evaluation of the CN-6000 analyzer was conducted for 10 tests including prothrombin time (PT), activated partial prothrombin time (aPTT), fibrinogen level, anti-Xa activity, and antithrombin activity using a unique portfolio of liquid ready-to-use reagents. Precision, sample and reagent carryovers, throughput, and sample turnaround time (STAT) function were prospectively assessed. Results from 343 samples (normal subjects, critically ill patients, patients receiving anticoagulants, subjects with high or low fibrinogen levels, and patients with decreased levels of factor II, V, VII, and X) were compared to those obtained on the STA-R Max 2® analyzer using dedicated reagents. Total precision (coefficient of variation) was below 7% for all parameters in both normal and pathological ranges. For all analyzed parameters, results obtained on the CN-6000 were strongly correlated with those obtained on the STA-R Max 2®analyzer. Agreement between both instruments was excellent for all assays. The CN-6000 demonstrated a 30% higher throughput compared to the STA-R Max 2® (258 vs 185 tests per hour for a panel of tests including PT, aPTT, fibrinogen, factor V, anti-Xa, and D-Dimer). STAT turnaround time for critical care samples testing was <7minutes. The CN-6000 analyzer performs equivalently or better than the STA-R Max 2® with a significantly improved throughput. This new hemostasis multiparameter analyzer appears to be particularly well suited for coagulation laboratories which require high sample throughput and manage high numbers of nonstandard and critical care samples.

Rapid Review: Diagnostic Accuracy of Pooled Testing versus Individual Testing Using RT-PCR for SARS-CoV-2 for Screening and Surveillance of Individuals with Suspected COVID-19

Background. Pooled testing has been implemented on a limited scale, mainly for screening and surveillance in populations with a low prevalence of COVID-19 to save on limited resources.&#x0D; Objective. To determine the diagnostic accuracy of pooled compared with individual RT-PCR testing for SARS-CoV-2 in individuals suspected of COVID-19.&#x0D; Methods. We searched websites of living CPGs on COVID-19 (Australian COVID-19, COVID NMA, CEBM Oxford), Philippine DOH HTA, databases (PubMed, CENTRAL, medRXIV/bioRXIV), and Clinicaltrials.gov for studies that used pooled testing on individuals suspected of COVID-19. When appropriate, we pooled data for sensitivity and specificity and obtained the range and median of other data, such as positive predictive value and resource savings. We did a priori subgroup analysis for pool size, presence or absence of symptoms and use case, type of specimen, cutoff for positivity, type of kit, and post hoc subgroup analysis for method of pooling and timing of processing.&#x0D; Results. We included 21 studies: 6 diagnostic accuracy studies, and 15 clinical validation studies. Studies had varying populations, index test kit and performance characteristics, positivity rate (0.02 to 15%), and pool size (5 to 16). There was moderate pooled sensitivity, 81% (95% CI 72, 88; I2=73.6%; 6 studies, 776 pools) and high pooled specificity, 99% (95% CI, 98 to 100; I2=1.84%; 5 studies, 666 pools). Positive predictive value based on 21 studies ranged from 67% to 100%. Resource savings in the number of test kits used ranged from 49 to 89%. Identified harms of pooled testing were delayed turnaround time for positive samples and laboratory errors.&#x0D; Conclusion. There is moderate sensitivity and high specificity with pooled testing for the screening of individuals with suspected COVID-19. We recommend further studies to validate the utility based on community prevalence and other test variables.