A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Mauro Petrillo*, Marco Fabbri, Dafni Maria Kagkli, Maddalena Querci, Guy Van den Eede, Erik Alm, Derya Aytan, Salvador Capella-Gutierrez, Catherine Carrillo, Alessandro Cestaro, Kok-Gan Chan, Teresa Coque, Christoph Endrullat, Ivo Gut, Paul Hammer, Gemma L. Kay, Jean-Yves Madec, Alison E. Mather, Alice Carolyn McHardy, Thierry NaasValentina Paracchini, Silke Peter, Arthur Pightling, Barbara Raffael, John Rossen, Etienne Ruppé, Robert Schlaberg, Kevin Vanneste, Lukas Weber, Henrik Westh, Alexandre Angers-Loustau

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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.
Original languageEnglish
Article number80
JournalF1000Research
Volume10
ISSN2046-1402
DOIs
Publication statusPublished - 2021

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