Title: The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
Authors: ANGERS ALEXANDREPETRILLO MAUROBENGTSSON-PALME JOHANBERENDONK THOMASBLAIS BURTONCHAN KOK-GANCOQUE TERESA MARIAHAMMER PAULHESS STEFANIEKAGKLI DAFNI MARIAKRUMBIEGEL CARSTENFERNANDEZ LANZA VALMADEC JEAN-YVESNAAS THIERRYO'GRADY JUSTINPARACCHINI VALENTINAROSSEN JOHNRUPPE ETIENNEVAMATHEVAN JESSICAVENTURI VITTORIOVAN DEN EEDE GUY
Citation: F1000 RESEARCH vol. 7 p. 459
Publisher: F1000 RESEARCH LTD.
Publication Year: 2018
JRC N°: JRC111024
ISSN: 2046-1402
URI: https://f1000research.com/articles/7-459/v1
http://publications.jrc.ec.europa.eu/repository/handle/JRC111024
DOI: 10.12688/f1000research.14509.1
Type: Articles in periodicals and books
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 about microorganisms and their virulence and resistance properties. 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 this 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 a continued quality control over this 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 strategy, in the specific context of identifying the molecular determinants of antimicrobial resistance, were identified. For each of the challenges, set of questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the monitoring in humans, animals, food and the environment, in line with the principles of a “One Health” approach.
JRC Directorate:Health, Consumers and Reference Materials

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