A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing
Document Type
Article
Publication Date
1-1-2022
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain 'live' (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines' implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community. © 2022 Petrillo M et al.
Keywords
Anti-Bacterial Agents, Benchmarking, Computational biology, Drug resistance, Bacterial, High-Throughput nucleotide Sequencing, antiinfective agent, antibiotic resistance, article, benchmarking, bioinformatics, high throughput sequencing, performance indicator, pipeline, plant defense, quality control, antibiotic resistance, biology, genetics, procedures
Divisions
InstituteofBiologicalSciences
Funders
Sigrid De Keersmaecker and Nancy Roosens,Tewodros Debebe
Publication Title
F1000Research
Volume
10
Issue
80
Publisher
F1000 Research Ltd