Evaluating EURL Reference Laboratories performance in bacterial sequencing in the 2020 DTU Genomic Proficiency Test.

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 EURL-AR network, a total of 22 laboratories from a total of 22 countries submitted WGS and meta-data. Eleven laboratories were identified as overall underperforming, having serious sequencing problems in one or more of up to 12 submitted sequences. We evaluate several QC metrics and their impact on widely used metrics N50 and number of contigs >200 bp. We likewise present quality thresholds for pathogens in this round of the DTU GPT, namely Campylobacter, Escherichia coli and Salmonella enterica.