Abstract:
Whole genome sequencing (WGS) enables complete characterization of bacterial pathogenic isolates at single nucleotide resolution,
making it the ultimate tool for routine surveillance and outbreak investigation. The lack of standardization, and the
variation regarding bioinformatics workflows and parameters, however, complicates interoperability among (inter)national laboratories.
We present a validation strategy applied to a bioinformatics workflow for Illumina data that performs complete characterization
of Shiga toxin-producing
Escherichia coli (STEC) isolates including antimicrobial resistance prediction, virulence
gene detection, serotype prediction, plasmid replicon detection and sequence typing. The workflow supports three commonly
used bioinformatics approaches for the detection of genes and alleles: alignment with blast+, kmer-based
read mapping with
KMA, and direct read mapping with SRST2. A collection of 131 STEC isolates collected from food and human sources, extensively
characterized with conventional molecular methods, was used as a validation dataset. Using a validation strategy specifically
adopted to WGS, we demonstrated high performance with repeatability, reproducibility, accuracy, precision, sensitivity
and specificity above 95 % for the majority of all assays. The WGS workflow is publicly available as a ‘push-button’
pipeline at
https:// galaxy. sciensano. be. Our validation strategy and accompanying reference dataset consisting of both conventional and
WGS data can be used for characterizing the performance of various bioinformatics workflows and assays, facilitating interoperability
between laboratories with different WGS and bioinformatics set-ups.
