A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing - Anses - Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail
Journal Articles F1000Research Year : 2022

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

1 JRC - European Commission - Joint Research Centre [Ispra]
2 JRC - European Commission - Joint Research Centre [Geel]
3 ECDC - European Centre for Disease Prevention and Control [Stockholm, Sweden]
4 National Food Institute [Kongens Lyngby, Danemark]
5 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
6 CFIA - Canadian Food Inspection Agency
7 FEM - Fondazione Edmund Mach - Edmund Mach Foundation [Italie]
8 UM - University of Malaya = Universiti Malaya [Kuala Lumpur, Malaisie]
9 JiangSu University
10 IRYCIS - Instituto Ramon y Cajal de Investigacion Sanitaria [Madrid, Spain]
11 CIBERESP - Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública = Consortium for Biomedical Research of Epidemiology and Public Health
12 MSD - Merck Sharp & Dohme Corp.
13 BIST - Barcelona Institute of Science and Technology
14 UPF - Universitat Pompeu Fabra [Barcelona]
15 Science & Technology, Federal Department of Defence, Civil Protection and Sport
16 Quadram Institute
17 AVB - Unité Antibiorésistance et Virulence Bactériennes
18 CAM - University of Cambridge [UK]
19 UEA - University of East Anglia [Norwich]
20 HZI - Helmholtz Centre for Infection Research
21 CNRARA/Service de Microbiologie - Centre National de Référence Associé de la Résistance aux Antibiotiques [Hôpital Bicêtre AP-HP]
22 Eberhard Karls Universität Tübingen = University of Tübingen
23 FDA - U.S. Food and Drug Administration
24 UMCG - University Medical Center Groningen [Groningen]
25 IAME (UMR_S_1137 / U1137) - Infection, Anti-microbiens, Modélisation, Evolution
26 University of Utah
27 Sciensano [Bruxelles]
28 UZH - Universität Zürich [Zürich] = University of Zurich
29 Johns Hopkins Bloomberg School of Public Health [Baltimore]
30 Hvidovre University Hospital [Hvidovre, Danemark]
31 European Commission Publications Office
Catherine Carrillo
Christoph Endrullat
Gemma Kay

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.

Domains

Bacteriology
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Dates and versions

anses-04388471 , version 1 (19-03-2024)

Identifiers

Cite

Mauro Petrillo, Marco Fabbri, Dafni Maria Kagkli, Maddalena Querci, Guy van den Eede, et al.. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Research, 2022, 10, pp.80. ⟨10.12688/f1000research.39214.2⟩. ⟨anses-04388471⟩
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