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The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

Journal article
Authors A. Angers-Loustau
M. Petrillo
Johan Bengtsson-Palme
T. Berendonk
B. Blais
K. G. Chan
T. M. Coque
P. Hammer
S. Heß
D. M. Kagkli
C. Krumbiegel
V. F. Lanza
J. Y. Madec
T. Naas
J. O'Grady
V. Paracchini
J. W. A. Rossen
E. Ruppé
J. Vamathevan
V. Venturi
G. Van den Eede
Published in F1000Research
Volume 7
Pages 459
ISSN 2046-1402
Publication year 2018
Published at Centre for antibiotic resistance research, CARe
Institute of Biomedicine, Department of Infectious Medicine
Pages 459
Language en
Keywords Antimicrobial resistance, benchmarking, bioinformatics, next-generation sequencing
Subject categories Infectious Medicine


Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms.  In the implementation of any novel technology for regulatory purposes, important considerations such as harmonisation, validation and quality assurance need to be addressed.  NGS technologies pose unique challenges in these regards, in part due to their reliance on bioinformatics for the processing and proper interpretation of the data produced.  Well-designed benchmark resources are thus needed to evaluate, validate and ensure continued quality control over the bioinformatics component of the process.  This concept was explored as part of a workshop on "Next-generation sequencing technologies and antimicrobial resistance" held October 4-5 2017.   Challenges involved in the development of such a benchmark resource, with a specific focus on identifying the molecular determinants of AMR, were identified. For each of the challenges, sets of unsolved questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the requirement for monitoring of AMR bacteria in humans, animals, food and the environment, which is aligned with the principles of a "One Health" approach.

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