Impact of wet-lab protocols on the quality of whole-genome short-read sequences from foodborne microbial pathogens

To analyze the extent of variability introduced by differing wet-lab procedures on the quality of the sequence data we conducted an interlaboratory study in the years 2021 and 2022, involving four bacterial pathogens, which account for the majority of food-related bacterial infections: Campylobacter spp., Escherichia coli, Listeria monocytogenes and Salmonella enterica. The participants, ranging from German federal research institutes, federal state laboratories to universities and companies, were asked to follow their routine in-house protocols for sequencing. Participants prepared and sequenced 10 isolates and one previously isolated DNA (control) per species, applying a broad range of library preparation kits. Sequencing platforms included Illumina's MiSeq, NextSeq, iSeq, NovaSeq and Thermo Fisher Scientific's Ion S5. Sequence and assembly quality was then analyzed centrally for individual samples. Additionally, SNP and cgMLST calling were performed to assess the reproducibility of sequence data for individual samples.