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

Angers-Loustau, Alexandre and Petrillo, Mauro and Bengtsson-Palme, Johan and Berendonk, Thomas and Blais, Burton and Chan, Kok Gan and Coque, Teresa M. and Hammer, Paul and Heß, Stefanie and Kagkli, Dafni M. and Krumbiegel, Carsten and Lanza, Val F. and Madec, Jean-Yves and Naas, Thierry and O'Grady, Justin and Paracchini, Valentina and Rossen, John W.A. and Ruppé, Etienne and Vamathevan, Jessica and Venturi, Vittorio and Van den Eede, Guy (2018) The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7. p. 459. ISSN 2046-1402

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Official URL: https://doi.org/10.12688/f1000research.14509.2

Abstract

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.

Item Type: Article
Uncontrolled Keywords: Antimicrobial resistance; bioinformatics; next-generation sequencing; benchmarking
Subjects: Q Science > Q Science (General)
Q Science > QH Natural history
Divisions: Faculty of Science > Institute of Biological Sciences
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 20 Sep 2019 04:00
Last Modified: 20 Sep 2019 04:00
URI: http://eprints.um.edu.my/id/eprint/22472

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