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How small modifications in laboratory workflow of blood cultures can have a significant impact on time to results

EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES 2018年第9期37卷 1753-1760页

作者： Van den Poel, B. Klak, A. Desmet, S. Verhaegen, J. Univ Hosp Leuven Dept Lab Med Leuven Belgium Univ Leuven KU Leuven Dept Microbiol & Immunol Herestr 49 B-3000 Leuven Belgium

Rapid identification and antimicrobial susceptibility testing of micro-organisms causing bloodstream infections is crucial in the management of septic patients. In this study, we compared a period of twice-daily and a period of thrice-daily reading of subculture agar plates. In 2016, 10,644 positive blood cultures bottles (bioMerieux) from 2608 patients were analyzed at UZ Leuven. Identification and antimicrobial susceptibility testing were performed by MALDI-TOF MS (Bruker Daltonics) and Vitek 2 (bioMerieux) respectively. In period 1 (January to June), subculture plates were read at 8:30 a.m. and 2:00 p.m. during the weekdays. In period 2 (August until December), reading was performed at 8:30 a.m., 2:00 p.m., and 5:00 p.m. Time to identification and time to AST results after positivity were compared. In period 1, median time to identification of all organisms was 22.8 h compared to 20.2 h in period 2 (p < 0.01). Moreover, micro-organisms were identified before 12 h in 9% of samples in period 2, a significant increase compared to 2% in period 1 (p < 0.01). In period 2, AST results were known within 36 h in 39% of samples, compared to 31% in period 1 (p < 0.01). Optimization of the reading frequency of subcultures of blood cultures significantly decreases time to results. Further optimization can be done by introducing lab automation. We will use the data of this study as a baseline to analyze the impact of introducing WASPLab (Copan Diagnostics) automation on time to results.

关键词： Rapid identification Antimicrobial susceptibility testing Blood cultures laboratory workflow Reading frequency

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4D Simulation System for laboratory workflow of Life Science Automation

4D Simulation System for Laboratory Workflow of Life Science...

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29th Annual IEEE International Instrumentation and Measurement Technology Conference (I2MTC)

作者： Li, Yanfei Junginger, Steffen Stoll, Norbert Thurow, Kerstin Ctr Life Sci Automat Rostock Germany Univ Rostock Inst Automat Rostock Germany

ISBN: (纸本)9781457717710

Due to the complex and distributed nature of high-end projects in Life Science Automation, it is still not possible to simulate workflows on laboratory workbenches frequently in a real time equivalent manner. It is crucial to ensure the availability of desired assays and automated workflows in advance. This paper presents the concept of a 4D simulation system, which synthesizes technologies as Process Control Software (PCS), Data Management System (DMS), programming technology, advanced CAD technology and some 3D animation tool to realize a dynamic simulation for laboratory workflow Management. The system would be flexible and controllable for automation assays, improve laboratory workflows, efficiency and accuracy, which would reduce the assays cost and the risks of rushing to unreasonable plans, and also improve the laboratory management level.

关键词： Life Science Automation laboratory workflow 4D Simulation

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Improvement of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of difficult-to-identify bacteria and its impact in the workflow of a clinical microbiology laboratory

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DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE 2014年第1期79卷 1-6页

作者： Rodriguez-Sanchez, Belen Marin, Mercedes Sanchez-Carrillo, Carlos Cercenado, Emilia Ruiz, Adrian Rodriguez-Creixems, Marta Bouza, Emilio Hosp Gen Univ Gregorio Maranon Inst Invest Sanit Gregorio Maranon Dept Clin Microbiol & Infect Dis Madrid Spain Univ Complutense Madrid Fac Med Madrid Spain

This study evaluates matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) capability for the identification of difficult-to-identify microorganisms. A total of 150 bacterial isolates inconclusively identified with conventional phenotypic tests were further assessed by 16S rRNA sequencing and by MALDI-TOF MS following 2 methods: a) a simplified formic acid-based, on-plate extraction and b) performing a tube-based extraction step. Using the simplified method, 29 isolates could not be identified. For the remaining 121 isolates (80.7%), we obtained a reliable identification by MALDI-TOF: in 103 isolates, the identification by 16S rRNA sequencing and MALDI TOF coincided at the species level (68.7% from the total 150 analyzed isolates and 85.1% from the samples with MALDI-TOF result), and in 18 isolates, the identification by both methods coincided at the genus level (12% from the total and 14.9% from the samples with MALDI-TOF results). No discordant results were observed. The performance of the tube-based extraction step allowed the identification at the species level of 6 of the 29 unidentified isolates by the simplified method. In summary, MALDI-TOF can be used for the rapid identification of many bacterial isolates inconclusively identified by conventional methods. (C) 2014 Elsevier Inc. All rights reserved.

关键词： MALDI-TOF Bacterial identification Difficult-to-identify bacteria 16S rRNA sequencing laboratory workflow

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Can I benefit from laboratory automation? A decision aid for the successful introduction of laboratory automation

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ANALYTICAL AND BIOANALYTICAL CHEMISTRY 2024年第1期416卷 5-19页

作者： Rupp, Nicole Ries, Robert Wienbruch, Rebecca Zuchner, Thole Albstadt Sigmaringen Univ Fac Life Sci Professorship Bioanalyt & Lab Automat Anton Gunther Str 51 D-72488 Sigmaringen Germany Boehringer Ingelheim Pharm GmbH & Co KG Drug Discovery Sci Birkendorfer Str 65 D-88397 Biberach An Der Riss Germany

The large volumes of samples to be analysed every day would be impossible to manage without laboratory automation. As laboratory procedures have progressed, so have the tasks of laboratory personnel. With this feature article, we would like to provide (bio)chemical practitioners with little or no knowledge of laboratory automation with a guide to help them decide whether to implement laboratory automation and find a suitable system. Especially in small- and medium-sized laboratories, operating a laboratory system means having bioanalytical knowledge, but also being familiar with the technical aspects. However, time, budget and personnel limitations allow little opportunity for personnel to get into the depths of laboratory automation. This includes not only the operation, but also the decision to purchase an automation system. Hasty investments do not only result in slow or non-existent cost recovery, but also occupy valuable laboratory space. We have structured the article as a decision tree, so readers can selectively read chapters that apply to their individual situation. This flexible approach allows each reader to create a personal reading flow tailored to their specific needs. We tried to address a variety of perspectives on the topic, including people who are either supportive or sceptical of laboratory automation, personnel who want or need to automate specific processes, those who are unsure whether to automate and those who are interested in automation but do not know which areas to prioritize. We also help to make a decision whether to reactivate or discard already existing and unused laboratory equipment.

关键词： laboratory automation Liquid handling Bioanalysis laboratory workflow Assay development Small- and medium-sized enterprises

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Implementing a laboratory Automation System: Experience of a Large Clinical laboratory

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JALA 2012年第1期17卷 16-23页

作者： Lam, Choong Weng Jacob, Edward Alexandra Hosp Dept Lab Med Singapore 159964 Singapore Singapore Gen Hosp Dept Pathol Singapore 0316 Singapore

Laboratories today face increasing pressure to automate their operations as they are challenged by a continuing increase in workload, need to reduce expenditure, and difficulties in recruitment of experienced technical staff. Was the implementation of a laboratory automation system (LAS) in the Clinical Biochemistry laboratory at Singapore General Hospital successful? There is no simple answer, so the following topics comparing and contrasting pre- and post-LAS have been explored: turnaround time (TAT), laboratory errors, and staff satisfaction. The benefits and limitations of LAS from the laboratory experience were also reviewed. The mean TAT for both stat and routine samples decreased post-LAS (30% and 13.4%, respectively). In the 90th percentile TAT chart, a 29% reduction was seen in the processing of stat samples on the LAS. However, no significant difference in the 90th percentile TAT was observed with routine samples. It was surprising to note that laboratory errors increased post-LAS. Considerable effort was needed to overcome the initial difficulties associated with adjusting to a new system, new software, and new working procedures. Although some of the known advantages and limitations of LAS have been validated, the claimed benefits such as improvements in TAT, laboratory errors, and staff morale were not evident in the initial months.

关键词： total laboratory automation laboratory automation system turnaround time laboratory workflow

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Fully digital pathology laboratory routine and remote reporting of oral and maxillofacial diagnosis during the COVID-19 pandemic: a validation study

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VIRCHOWS ARCHIV 2021年第3期479卷 585-595页

作者： Araujo, Anna Luiza Damaceno do Amaral-Silva, Gleyson Kleber Perez-de-Oliveira, Maria Eduarda Gallagher, Karen Patricia Dominguez Lopez de Caceres, Cinthia Veronica Bardalez Roza, Ana Luiza Oliveira Correa Leite, Amanda Almeida Mariz, Bruno Augusto Linhares Almeida Rodrigues-Fernandes, Carla Isabelly Fonseca, Felipe Paiva Lopes, Marcio Ajudarte Speight, Paul M. Khurram, Syed Ali Jorge Junior, Jacks Martins, Manoela Domingues de Almeida, Oslei Paes Santos-Silva, Alan Roger Vargas, Pablo Agustin Univ Campinas UNICAMP Piracicaba Dent Sch Semiol & Oral Pathol Areas Oral Diag Dept Av Limeira 901 BR-13414903 Piracicaba SP Brazil Fed Univ Minas Gerais UFMG Sch Dent Dept Oral Surg & Pathol Belo Horizonte MG Brazil Univ Sheffield Sch Clin Dent Unit Oral & Maxillofacial Pathol Sheffield S Yorkshire England Univ Fed Rio Grande do Sul Sch Dent Dept Oral Pathol Porto Alegre RS Brazil

The role of digital pathology in remote reporting has seen an increase during the COVID-19 pandemic. Recently, recommendations had been made regarding the urgent need of reorganizing head and neck cancer diagnostic services to provide a safe work environment for the staff. A total of 162 glass slides from 109 patients over a period of 5 weeks were included in this validation and were assessed by all pathologists in both analyses (digital and conventional) to allow intraobserver comparison. The intraobserver agreement between the digital method (DM) and conventional method (CM) was considered almost perfect (kappa ranged from 0.85 to 0.98, with 95% CI, ranging from 0.81 to 1). The most significant and frequent disagreements within trainees encompassed epithelial dysplasia grading and differentiation among severe dysplasia (carcinoma in situ) and oral squamous cell carcinoma. The most frequent pitfall from DM was lag in screen mirroring. The lack of details of inflammatory cells and the need for a higher magnification to assess dysplasia were pointed in one case each. The COVID-19 crisis has accelerated and consolidated the use of online meeting tools, which would be a valuable resource even in the post-pandemic scenario. Adaptation in laboratory workflow, the advent of digital pathology and remote reporting can mitigate the impact of similar future disruptions to the oral and maxillofacial pathology laboratory workflow avoiding delays in diagnosis and report, to facilitate timely management of head and neck cancer patients.

关键词： Remote reporting COVID-19 Digital microscopy Oral and maxillofacial pathology Digital pathology laboratory workflow

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Pipette Show: An Open Source Web Application to Support Pipetting into Microplates

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ACS SYNTHETIC BIOLOGY 2022年第2期11卷 996-999页

作者： Falk, Johannes Mendler, Marc Kabisch, Johannes Jacobs Univ Bremen Dept Life Sci & Chem D-28759 Bremen Germany Tech Univ Darmstadt Inst Phys Kondensierter Materie D-64289 Darmstadt Germany Trondheim Gloshaugen NTNU Dept Biotechnol & Food Sci N-7034 Trondheim Norway Tech Univ Darmstadt Comp Aided Synthet Biol D-64289 Darmstadt Germany

Despite increasing automation, manual pipetting remains a daily important task in life science laboratories. However, the creation of an efficient work plan is often time-consuming, and its completion is error-prone. Here, we present Pipette Show, a free *** based application that optimizes the generation of an efficient work plan for pipetting into microplates and supports its reliable execution by visual guidance. The basis forms a graphical web interface with a module for building workflows as well as a module displaying the information for each pipetting step by illuminating wells of microplates placed on a tablet.

关键词： laboratory workflow microplates digital lab deskilling reproducibility

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Integration of Diagnostic Microbiology in a Model of Total laboratory Automation

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laboratory MEDICINE 2016年第1期47卷 73-82页

作者： Da Rin, Giorgio Zoppelletto, Maira Lippi, Giuseppe Bassano del Grappa Gen Hosp Serv Lab Med Bassano Del Grappa VI Italy Acad Hosp Parma Lab Clin Chem & Hematol Parma Italy

Background: Although automation has become widely utilized in certain areas of diagnostic testing, its adoption in diagnostic microbiology has proceeded much more slowly. Objective: To describe our real-world experience of integrating an automated instrument for diagnostic microbiology (Walk-Away Specimen Processor, WASPLab) within a model of total laboratory automation (TLA). Methods: The implementation process was divided into 2 phases. The former period, lasting approximately 6 weeks, entailed the installation of the WASPLab processor to operate as a standalone instrumentation, whereas the latter, lasting approximately 2 weeks, involved physical connection of the WASPLab with the automation. Results: Using the WASPLab instrument in conjunction with the TLA model, we obtained a time savings equivalent to the work of 1.2 full-time laboratory technicians for diagnostic microbiology. The connection of WASPLab to TLA allowed its management by a generalist or clinical chemistry technician, with no need for microbiology skills on the part of either worker. Hence, diagnostic microbiology could be performed by the staff that is already using the TLA, extending their activities to include processing urgent clinical chemistry and hematology specimens. The time to result was also substantially improved. Conclusions: According to our experience, using the WASPLab instrument as part of a TLA in diagnostic microbiology holds great promise for optimizing laboratory workflow and improving the quality of testing.

关键词： total laboratory automation laboratory automation system laboratory workflow microbiology efficiency diagnostic system

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Compliance of clinical microbiology laboratories with recommendations for the diagnosis of bloodstream infections: Data from a nationwide survey in Italy

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MICROBIOLOGYOPEN 2020年第4期9卷 e1002-e1002页

作者： Arena, Fabio Argentieri, Marta Bernaschi, Paola Fortina, Giacomo Kroumova, Vesselina Pecile, Patrizia Rassu, Mario Spanu, Teresa Rossolini, Gian Maria Fontana, Carla Univ Foggia Dept Clin & Expt Med Foggia Italy Don Carlo Gnocchi Fdn IRCCS Florence Italy Childrens Hosp Bambino Gesu Microbiol Unit Rome Italy Italian Work Grp Infect Crit Ill Patient GliPac A Milan Italy Univ Hosp Maggiore della Carita Infect Control Unit Novara Italy Florence Careggi Univ Hosp Clin Microbiol & Virol Unit Florence Italy S Bortolo Hosp AULS 8 Berica Microbiol & Virol Lab Vicenza Italy Univ Cattolica Sacro Cuore Fdn Policlin Univ Agostino Gemelli Inst Microbiol Rome Italy Univ Florence Dept Expt & Clin Med Florence Italy Univ Roma Tor Vergata Dept Expt Med Via Montpellier 1 I-00133 Rome Italy Tor Vergata Univ Hosp Microbiol & Virol Lab Rome Italy

In 2014, the Italian Working Group for Infections in Critically Ill Patient of the Italian Association of Clinical Microbiologists updated the recommendations for the diagnostic workflow for bloodstream infections (BSI). Two years after publication, a nationwide survey was conducted to assess the compliance with the updated recommendations by clinical microbiology laboratories. A total of 168 microbiologists from 168 laboratories, serving 204 acute care hospitals and postacute care facilities, were interviewed during the period January-October 2016 using a questionnaire consisting of nineteen questions which assessed the level of adherence to various recommendations. The most critical issues were as follows: (a) The number of sets of blood cultures per 1,000 hospitalization days was acceptable in only 11% of laboratories;(b) the minority of laboratories (42%) was able to monitor whether BCs were over or under-inoculated;(c) among the laboratories monitoring BC contamination (80%), the rate of contaminated samples was acceptable in only 12% of cases;(d) the Gram-staining results were reported within 1 hr since BC positivity in less than 50% of laboratories. By contrast, most laboratories received vials within 2-4 hr from withdrawal (65%) and incubated vials as soon as they were received in the laboratory (95%). The study revealed that compliance with the recommendations is still partial. Further surveys will be needed to monitor the situation in the future.

关键词： bacteraemia blood cultures laboratory workflow quality standardization

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Supernatant fluid from endobronchial ultrasound-guided transbronchial needle aspiration for rapid next-generation sequencing

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Journal of the American Society of Cytopathology 2024年第5期13卷 340-345页

作者： Jager, Lucy Jennings, Lawrence J. Dittmann, David Blanco, Jayjay Choy, Bonnie Nayar, Ritu Department of Pathology Northwestern University Feinberg School of Medicine Northwestern Memorial Hospital Chicago Illinois United States

Introduction: There is an increasing demand to optimize the workflow and maximize tissue available for next-generation sequencing (NGS) for non-small cell carcinoma. We looked at transbronchial needle endobronchial ultrasound-guided bronchoscopy with transbronchial needle aspiration samples and evaluated the performance of supernatant (SN) fluid processed from a dedicated aspirate collected for NGS testing. Materials and methods: Nineteen samples were collected and processed using a new workflow. Five aspirates were collected in formalin. One additional dedicated pass was collected fresh and centrifuged. The resulting cell pellet was added to formalin for cell block (CB) processing. DNA and RNA were extracted from concentrated SN for targeted testing using the Oncomine Precision Assay (Thermo Scientific, Waltham, MA). NGS results from the corresponding CB samples were used as “controls” for comparison. Results: Thirty-one mutations were detected in SN (Table 1). The most frequently mutated genes were TP53 (35%), EGFR (23%), KRAS (13%), CTNNB1 (6%), and ERBB2 (6%). There was 100% concordance between the mutations detected in SN and corresponding CBs with comparable variant allele frequencies. Turnaround time of NGS results was 1 day for SN compared to 4-10 days for CB. Conclusions: We were able to demonstrate the usefulness of SN for reliable rapid molecular results. We successfully incorporated the workflow for tissue handling and processing among our clinical, cytopathology, and molecular teams. Molecular results were available at the same time as the cytologic diagnosis, allowing for timely reporting of a comprehensive diagnosis. This approach is particularly useful in patients with advanced disease requiring urgent management. © 2024 American Society of Cytopathology

关键词： EBUS-TBNA laboratory workflow Next-generation sequencing Non-small cell carcinoma Supernatant

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