The 2020 DTU genomic proficiency test for the network of SeqAfrica

Currently, the global surveillance and outbreak investigation of bacterial pathogens including antimicrobial resistance is amidst a paradigm shift from traditional microbiology to bioinformatics. This is due to the global need to ensure that the quality of data being produced is reliable and enables risk managers to act on trusted data. Thus, it is essential there is a mechanism to setup an inter-laboratory whole genome sequencing (WGS) proficiency test (PT) scheme to meet the demand in evaluating laboratories capability to produce reliable genomic data and work towards accrediting the methodology. From the SeqAfrica network, 4 laboratories submitted WGS and meta-data. We evaluate several QC metrics and present quality thresholds for pathogens in this round of the DTU GPT, namely Staphylococcus, Escherichia coli, Campylobacter, Salmonella, Enterococcus faecalis and Enterococcus faecium.