Following a brainstorming workshop organised by the JRC in 2017, experts compiled the challenges related to a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants. A focus was placed on the implementation of next-generation sequencing technologies to monitor the rise and spread of antimicrobial resistance.
The phenomenon of antimicrobial resistance (AMR) refers to the ability of microorganisms to resist antimicrobial treatments, such as modern antibiotics.
Its spread represents a clear threat for human and animal health, and places a significant burden on the current healthcare systems.
International action plans to fight AMR rely on the implementation of efficient schemes for monitoring the appearance and spread of new resistant bacteria. It is worth to mention that the European Commission has adopted an EU One Health Action Plan against AMR.
As the detection of AMR can be achieved through characterisation of the bacteria genomes, new DNA sequencing technologies have the potential to become important tools in future surveillance frameworks. To discuss the further challenges, the JRC organised two brainstorming workshops (March 2017 and October 2017) involving top experts representing the different fields where a lot of activities are currently ongoing to develop methods that rely on NGS technologies to detect AMR: human health, veterinary health, food control and environmental monitoring.
A substantial part of the discussions was dedicated to evaluating the possibility of developing a harmonised "benchmark" resource that could be used to evaluate, compare and validate strategies as they are developed, in order to eventually implement them in a broader and harmonised context. By comprehensively framing the problems ahead, this 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.
Read more in:
- Angers-Loustou et al.: The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies, F1000 Research Open for Science (2018), doi: 10.12688/f1000research.14509.1
- European Commission action plan against AMR
- The Role and Implementation of NGS Technologies in the Coordinated Action Plan against AMR (workshop report)
- 1 August 2018