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

Alexandre Angers-Loustau, Mauro Petrillo, Johan Bengtsson-Palme, Thomas Berendonk, Burton Blais, Kok-Gan Chan, Teresa M. Coque, Paul Hammer, Stefanie Heß, Dafni M. Kagkli, Carsten Krumbiegel, Val F. Lanza, Jean-Yves Madec, Thierry Naas, Justin O'Grady, Valentina Paracchini, John W.A. Rossen, Etienne Ruppé, Jessica Vamathevan, Vittorio Venturi, Guy Van den Eede
  • F1000Research, April 2018, F1000Research
  • DOI: 10.12688/f1000research.14509.1

How to evaluate genomics approaches developed to detect antibiotics resistance?

What is it about?

Our mission in the Joint Research Centre of the European Commission is to support EU policies with independent evidence throughout the whole policy cycle. As such, we have been hosting different workshops in 2017 discussing the state of the art and the potential of using Next-Generation Sequencing (NGS) in the detection and monitoring of antimicrobial resistance (AMR). The discussions involved top experts in the field, across the different disciplines (human health, veterinary health, food control and environmental monitoring). A substantial part of the debate was dedicated to evaluating the possibility of developing a harmonised benchmark strategy (with the associated data and criteria to be used) for bioinformatics pipelines that are used to identify the genetic determinants of AMR in a sequenced sample. The article summarises the discussions and provides a reflection on the identified challenges.

Why is it important?

By comprehensively framing the problems ahead, this article is an important step in eventually solving them. A well-designed benchmark will be of crucial importance in the field, not only for laboratories to evaluate their current procedures, but also in future discussions related to the harmonisation and validation of databases, tools and procedures to be used in implementing the technology for regulatory use.


Alexandre Angers-Loustau (Author)
Joint Research Centre, European Commission

Publishing this article on an open platform like F1000Research is a good way to engage in these discussions with the target audience, and foster interest in coordinated efforts (by ourselves and others) for the necessary follow-up activities.

The following have contributed to this page: Professor Teresa M. Coque, Professor Thierry Naas, Alexandre Angers-Loustau, Valentina Paracchini, and Dafni Maria Kagkli