The DTU Genomic Proficiency Test 2023
Global surveillance and outbreak investigation of bacterial pathogens, including monitoring for antimicrobial resistance, is undergoing a paradigm shift from traditional microbiology to bioinformatics. This transition is driven by the need for reliable sequencing data that empowers risk managers to make informed decisions. We have established an inter-laboratory Whole Genome Sequencing (WGS) Proficiency Test (PT) scheme to address this. As part of this scheme, three Genomic PT (GPT) test strains, belonging to Escherichia coli, Salmonella, and Staphylococcus, are provided in transport swabs. Participating countries must sequence these strains and analyze the resulting data to determine the sequence type using multilocus sequence typing (MLST), antimicrobial resistance (AMR) phenotypes and genotypes, and plasmid replicons. We evaluate both the raw sequencing reads and the subsequent analysis.