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

Publikation: Beitrag in FachzeitschriftForschungsartikelBeigetragenBegutachtung


  • Alexandre Angers-Loustau - , European Commission Joint Research Centre Institute (Autor:in)
  • Mauro Petrillo - , European Commission Joint Research Centre Institute (Autor:in)
  • Johan Bengtsson-Palme - , University of Gothenburg (Autor:in)
  • Thomas Berendonk - , Professur für Limnologie (Gewässerökologie), Institut für Hydrobiologie (Autor:in)
  • Burton Blais - , Canadian Food Inspection Agency (Autor:in)
  • Kok Gan Chan - , Jiangsu University, University of Malaya (Autor:in)
  • Teresa M. Coque - , Hospital Ramon y Cajal (Autor:in)
  • Paul Hammer - , (Autor:in)
  • Stefanie Heß - , Professur für Allgemeine Mikrobiologie, Professur für Limnologie (Gewässerökologie) (Autor:in)
  • Dafni M. Kagkli - , European Commission Joint Research Centre Institute (Autor:in)
  • Carsten Krumbiegel - , (Autor:in)
  • Val F. Lanza - , Hospital Ramon y Cajal (Autor:in)
  • Jean Yves Madec - , Unité Antibiorésistance et Virulence Bactériennes (Autor:in)
  • Thierry Naas - , Assistance publique – Hôpitaux de Paris (Autor:in)
  • Justin O'Grady - , University of East Anglia (Autor:in)
  • Valentina Paracchini - , European Commission Joint Research Centre Institute (Autor:in)
  • John W.A. Rossen - , University of Groningen (Autor:in)
  • Etienne Ruppé - , Institut national de la santé et de la recherche médicale (Autor:in)
  • Jessica Vamathevan - , European Molecular Biology Laboratory (EMBL) (Autor:in)
  • Vittorio Venturi - , International Centre for Genetic Engineering and Biotechnology (Autor:in)
  • Guy Van den Eede - , European Commission Joint Research Centre Institute (Autor:in)


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.


PublikationsstatusVeröffentlicht - 2018

Externe IDs

Scopus 85049602454
PubMed 30026930


Ziele für nachhaltige Entwicklung


  • Antimicrobial resistance, Benchmarking, Bioinformatics, Next-generation sequencing