The paper contains a brief overview of next-generation sequencing platforms and tools, the resources that can be used to detect and quantify resistance from sequencing data, and descriptions of applications in clinical genomics, clinical/human metagenomics as well as in environmental settings (the latter being the part where I contributed the most). Compared to much of the writing on antibiotic resistance and sequencing applications, I think this paper is pretty easily accessible to a general audience.
I first met Etienne on the JRC workshops for how next-generation sequencing could be implemented in the EU’s Coordinated Action Plan against Antimicrobial Resistance (2,3), and it seems quite fitting that we now ended up writing a paper on such implementations together.
Ruppé E, Bengtsson-Palme J, Charretier Y, Schrenzel J: How next-generation sequencing can address the antimicrobial resistance challenge. AMR Control, 2019-20, 60-65 (2019). [Paper link]
Angers A, Petrillo P, Patak, A, Querci M, Van den Eede G: The Role and Implementation of Next-Generation Sequencing Technologies in the Coordinated Action Plan against Antimicrobial Resistance. JRC Conference and Workshop Report, EUR 28619 (2017). doi: 10.2760/745099[Link]
Angers-Loustau A, Petrillo M, Bengtsson-Palme J, Berendonk T, Blais B, Chan KG, Coque TM, Hammer P, Heß S, Kagkli DM, Krumbiegel C, Lanza VF, Madec J-Y, Naas T, O’Grady J, Paracchini V, Rossen JWA, Ruppé E, Vamathevan J, Venturi V, Van den Eede G: The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Research, 7, 459 (2018). doi: 10.12688/f1000research.14509.2[Paper link]