After the successful introduction of Next-Generation Sequencing (NGS) technology for epidemiological inference and surveillance in routine microbiology, laboratories face a new challenge as metagenomics for identification of pathogens and antimicrobial resistance genes is about to enter the laboratory. The programme highlights opportunities and challenges posed by this technology. The workshop has been designed to boost practical knowledge exchange (with respect to both “wet-lab” and “e-lab”) as well as ample discussions with colleagues from all over the world.