CLSI Methods Development and Standardization Working Group Best Practices for Evaluation of Antimicrobial Susceptibility Tests.
Ontology highlight
ABSTRACT:
SUBMITTER: Humphries RM
PROVIDER: S-EPMC5869819 | biostudies-other | 2018 Apr
REPOSITORIES: biostudies-other
Publications
CLSI Methods Development and Standardization Working Group Best Practices for Evaluation of Antimicrobial Susceptibility Tests.
Humphries Romney M RM Ambler Jane J Mitchell Stephanie L SL Castanheira Mariana M Dingle Tanis T Hindler Janet A JA Koeth Laura L Sei Katherine K
Journal of clinical microbiology 20180326 4
Effective evaluations of antimicrobial susceptibility tests (ASTs) require robust study design. The Clinical and Laboratory Standards Institute (CLSI) Subcommittee on Antimicrobial Susceptibility Testing has recognized that many published studies reporting the performance of commercial ASTs (cASTs) suffer from major design and/or analysis flaws, rendering the results difficult or impossible to interpret. This minireview outlines the current consensus of the Methods Development and Standardizatio ...[more]
Similar Datasets
Project description:The performance of a disk diffusion test using broth from positive blood cultures as inoculum (direct disk diffusion [dDD]) was evaluated for a collection of 20 challenge isolates of Enterobacteriaceae, Acinetobacter baumannii, and Pseudomonas aeruginosa Isolates seeded into human blood were inoculated into Bactec Plus Aerobic/F, VersaTREK Redox 1, and BacT/Alert FA Plus bottles and incubated in the respective automated blood culture systems. Disk diffusion results were compared to reference disk diffusion results. Categorical agreement (CA) values for dDD, after removal of random errors due to natural MIC variation, were 87.8%, 88.4%, and 92.2% for the BacT/Alert, Bactec, and VersaTREK systems, respectively. No very major errors (VME) were observed, and major error (ME) rates were 3.0%, 2.3%, and 1.7%, respectively. Incubation of the dDD test samples for 6 h compared to incubation for 16 to 18 h resulted in 19.9% of tests having too light of growth to allow reading of zones of inhibition. Among the evaluable dDD tests, CA values were 58.9%, 76.6%, and 73.2% for the isolates seeded into the BacT/Alert, Bactec, and VersaTREK systems, respectively. VME rates for isolates seeded into these systems were 2.2%, 1.8%, and 3.0%, respectively, and ME rates were 25.4%, 6.1%, and 2.8%, respectively, at the 6-h reading. The best performance of dDD was found for blood cultures with bacterial concentrations in the range of 7.6 × 107 to 5.0 × 108 CFU/ml; CA values ranged from 94.7 to 96.2% for these concentrations after 18 h of incubation and from 76.9 to 84.1% after 6 h of incubation. These preliminary data demonstrate the potential accuracy of dDD testing by the clinical laboratory.
| S-EPMC5824059 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-06-08 | GSE107768 | GEO
Project description:Enhanced cross-linking immunoprecipitation (eCLIP) featuring a size-matched input control has been recently applied to profile the binding sites of more than one hundred RNA binding proteins (RBPs). However computational pipelines and quality control metrics needed to process CLIP data at scale have yet to be well defined. Here, we describe our ENCODE eCLIP processing pipeline (https://github.com/YeoLab/eclip), enabling users to go from raw reads to processed peaks that are enriched above paired input, reproducible across biological replicates, and can be directly compared against the public ENCODE eCLIP resource. In particular, we discuss processing steps designed to address common artifacts, including properly quantifying unique RNA fragments bound by both unique genomic- and repetitive element-mapped reads. Using manual quality annotation of 350 ENCODE eCLIP experiments, we develop metrics for quality assessment of eCLIP experiments prior to and after sequencing, including library yield, number of unique fragments in the library, total binding relative information, and biological reproducibility. In particular, we quantify the commonly believed linkage between depth of sequencing and peak discovery, and derive methods for estimating required sequencing depth based on pre-sequencing metrics. Finally we provide recommendations for the common question of integrating RBP binding information with RNA-seq to generate splicing maps representing the positional effect of binding on alternative splicing. These pipelines and QC metrics enable large-scale processing and analysis of eCLIP data, and will help to standardize rigorous analysis of RBP binding data.
2018-06-08 | GSE107767 | GEO
Project description:Enhanced cross-linking immunoprecipitation (eCLIP) featuring a size-matched input control has been recently applied to profile the binding sites of more than one hundred RNA binding proteins (RBPs). However computational pipelines and quality control metrics needed to process CLIP data at scale have yet to be well defined. Here, we describe our ENCODE eCLIP processing pipeline (https://github.com/YeoLab/eclip), enabling users to go from raw reads to processed peaks that are enriched above paired input, reproducible across biological replicates, and can be directly compared against the public ENCODE eCLIP resource. In particular, we discuss processing steps designed to address common artifacts, including properly quantifying unique RNA fragments bound by both unique genomic- and repetitive element-mapped reads. Using manual quality annotation of 350 ENCODE eCLIP experiments, we develop metrics for quality assessment of eCLIP experiments prior to and after sequencing, including library yield, number of unique fragments in the library, total binding relative information, and biological reproducibility. In particular, we quantify the commonly believed linkage between depth of sequencing and peak discovery, and derive methods for estimating required sequencing depth based on pre-sequencing metrics. Finally we provide recommendations for the common question of integrating RBP binding information with RNA-seq to generate splicing maps representing the positional effect of binding on alternative splicing. These pipelines and QC metrics enable large-scale processing and analysis of eCLIP data, and will help to standardize rigorous analysis of RBP binding data.
2018-06-08 | GSE107766 | GEO
Project description:This submission is a dataset of single-nucleus multi-omics of uninjured and injured spinal cords of mice harvested and profiled using 10x Multiome ATAC + Gene Expression kit.
2024-04-30 | GSE230765 | GEO
Project description:R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution significantly impacts genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here we review the main existing methodologies underlying R-loop mapping and assess their limitations and the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we offer a possible resolution to the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.
2021-02-24 | GSE158480 | GEO
Project description:BackgroundRapid diagnostic tests (RDTs) largely account for the scale-up of malaria diagnosis in endemic settings. However, diversity in labelling including the instructions for use (IFU) limits their interchangeability and user-friendliness. Uniform, easy to follow and consistent labelling, aligned with international standards and appropriate for the level of the end user's education and training, is crucial but a consolidated resource of information regarding best practices for IFU and labelling of RDT devices, packaging and accessories is not available.MethodsThe Roll Back Malaria Partnership (RBM) commissioned the compilation of international standards and regulatory documents and published literature containing specifications and/or recommendations for RDT design, packaging and labelling of in vitro diagnostics (IVD) (which includes RDTs), complemented with a questionnaire based survey of RDT manufacturers and implementers. A summary of desirable RDT labelling characteristics was compiled, which was reviewed and discussed during a RBM Stakeholder consultation meeting and subsequently amended and refined by a dedicated task force consisting of country programme implementers, experts in RDT implementation, IVD regulatory experts and manufacturers.ResultsThis process led to the development of consensus documents with a list of suggested terms and abbreviations as well as specifications for labelling of box, device packaging, cassettes, buffer bottle and accessories (lancets, alcohol swabs, transfer devices, desiccants). Emphasis was placed on durability (permanent printing or water-resistant labels), legibility (font size, letter type), comprehension (use of symbols) and ease of reference (e.g. place of labelling on the box or cassette packaging allowing quick oversight). A generic IFU template was developed, comprising background information, a template for procedure and reading/interpretation, a selection of appropriate references and a symbol key of internationally recognized symbols together with suggestions about appropriate lay-out, style and readability.ConclusionsThe present document together with its additional files compiled proposes best practices in labelling and IFU for malaria RDTs. It is expected that compliance with these best practices will increase harmonization among the different malaria RDT products available on the market and improve their user-friendliness.
| S-EPMC4302121 | biostudies-literature
Project description:Obtaining a research participant's voluntary and informed consent is the bedrock of sound ethics practice. Greater inclusion of children in research has led to questions about how paediatric consent operates in practice to accord with current and emerging legal and socio-ethical issues, norms, and requirements.Employing a qualitative thematic content analysis, we examined paediatric consent forms from major academic centres and public organisations across Canada dated from 2008-2011, which were purposively selected to reflect different types of research ethics boards, participants, and studies. The studies included biobanking, longitudinal studies, and gene-environment studies. Our purpose was to explore the following six emerging issues: (1) whether the scope of parental consent allows for a child's assent, dissent, or future consent; (2) whether the concepts of risk and benefit incorporate the child's psychological and social perspective; (3) whether a child's ability to withdraw is respected and to what extent withdrawal is permitted; (4) whether the return of research results includes individual results and/or incidental findings and the processes involved therein; (5) whether privacy and confidentiality concerns adequately address the child's perspective and whether standard data and/or sample identifiability nomenclature is used; and (6) whether retention of and access to paediatric biological samples and associated medical data are addressed.The review suggests gaps and variability in the consent forms with respect to addressing each of the six issues. Many forms did not discuss the possibility of returning research results, be they individual or general/aggregate results. Forms were also divided in terms of the scope of parental consent (specific versus broad), and none discussed a process for resolving disputes that can arise when either the parents or the child wishes to withdraw from the study.The analysis provides valuable insight and evidence into how consent forms address current ethical issues. While we do not thoroughly explore the contexts and reasons behind consent form gaps and variability, we do advocate and formulate the development of best practices for drafting paediatric health research consent forms. This can greatly ameliorate current gaps and facilitate harmonised and yet contextualised approaches to paediatric health research ethics.
| S-EPMC3571865 | biostudies-other
Project description:Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing platforms requires careful attention to detail for robust results. Thus far, much of the scientific Communit's focus for use in bacterial genomics has been on evaluating genome assembly algorithms and rigorously validating assembly program performance. Missing, however, is a focus on critical evaluation of variant callers for these genomes. Variant calling is essential for comparative genomics as it yields insights into nucleotide-level organismal differences. Variant calling is a multistep process with a host of potential error sources that may lead to incorrect variant calls. Identifying and resolving these incorrect calls is critical for bacterial genomics to advance. The goal of this review is to provide guidance on validating algorithms and pipelines used in variant calling for bacterial genomics. First, we will provide an overview of the variant calling procedures and the potential sources of error associated with the methods. We will then identify appropriate datasets for use in evaluating algorithms and describe statistical methods for evaluating algorithm performance. As variant calling moves from basic research to the applied setting, standardized methods for performance evaluation and reporting are required; it is our hope that this review provides the groundwork for the development of these standards.
| S-EPMC4493402 | biostudies-literature
Project description:ImportanceThe American Urological Association guidelines recommend 24 or fewer hours of antimicrobial prophylaxis for most urologic procedures. Continuing antimicrobial therapy beyond 24 hours may carry more risks than advantages.ObjectivesTo assess guideline discordance of antimicrobial prophylaxis for common urologic endoscopic procedures, and to identify opportunities for improving antimicrobial prescribing through future stewardship interventions.Design, setting, and participantsThis multicenter cohort study conducted manual audits of medical records of 375 patients who underwent 1 of 3 urologic procedures (transurethral resection of bladder tumor [TURBT], transurethral resection of the prostate [TURP], and ureteroscopy [URS]) at 5 Veterans Health Administration facilities from January 1, 2016, to June 30, 2017. Antimicrobial prescribing practices across the national Veterans Health Administration system were assessed using the administrative data for 29?530 records.Main outcomes and measuresGuideline discordance was assessed in the medical record review. Excessive postprocedural antimicrobial use was measured in the national administrative data analysis.ResultsThe medical records of a total of 375 patients were manually reviewed. Among the 375 patients, 366 (97.6%) were male and 9 (2.4%) were female, with a mean (SD) age of 64.2 (10.9) years and a predominantly white race/ethnicity (289 [77.1%]). In addition, 29?530 patient records in the national administrative database were assessed. Among the patient records, 28?938 (98.0%) were male and 592 (2.0%) were female with a mean (SD) age of 69.1 (10.2) years and a predominantly white race/ethnicity (23?297 [78.9%]). Among the manually reviewed medical records, periprocedural or postprocedural antimicrobial prescribing was guideline discordant in 217 patients (57.9%). Postprocedural antimicrobial agents were continued beyond 24 hours in 211 patients (56.3%) and were guideline discordant in 177 patients (83.9%), with a median (interquartile range) duration of 3 (3-5) days of unnecessary antimicrobial therapy. In the analysis of national administrative data, excessive postprocedural antimicrobial agents were prescribed in 10?988 of 29?350 patient records (37.2%), with a median (interquartile range) of 3 (2-6) excess days. For any given facility, a statistically significant correlation was observed in the frequency of postprocedural antimicrobial prescribing between any 2 procedures, indicating that facilities with higher rates of excessive use for 1 procedure also had higher rates for another procedure: TURP and TURBT (??=?0.719; 95% CI, 0.603-0.803; P?<?.001), TURP and URS (??=?0.629; 95% CI, 0.476-0.741; P?<?.001), and TURBT and URS (??=?0.813; 95% CI, 0.724-0.873; P?<?.001).Conclusions and relevanceIn this study of patients who underwent common urologic procedures, the rate of guideline-discordant antimicrobial use was high mostly because of overprescribing of postprocedural antimicrobial agents; future antimicrobial stewardship interventions should target the postprocedural period.
| S-EPMC6324350 | biostudies-literature