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

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.

ANGERS Alexandre;  PETRILLO Mauro;  BENGTSSON-PALME Johan;  BERENDONK Thomas;  BLAIS Burton;  CHAN Kok-Gan;  COQUE Teresa Maria;  HAMMER Paul;  HESS Stefanie;  KAGKLI Dafni Maria;  KRUMBIEGEL Carsten;  FERNANDEZ LANZA Val;  MADEC Jean-Yves;  NAAS Thierry;  O'GRADY Justin;  PARACCHINI Valentina;  ROSSEN John;  RUPPE Etienne;  VAMATHEVAN Jessica;  VENTURI Vittorio;  VAN DEN EEDE Guy; 

2018-07-24

F1000 RESEARCH LTD.

JRC111024

2046-1402,   

https://f1000research.com/articles/7-459/v1,    https://publications.jrc.ec.europa.eu/repository/handle/JRC111024,   

10.12688/f1000research.14509.1,