<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bert Bogaerts</style></author><author><style face="normal" font="default" size="100%">Stéphanie Nouws</style></author><author><style face="normal" font="default" size="100%">Bavo Verhaegen</style></author><author><style face="normal" font="default" size="100%">Sarah Denayer</style></author><author><style face="normal" font="default" size="100%">Julien Van Braekel</style></author><author><style face="normal" font="default" size="100%">Raf Winand</style></author><author><style face="normal" font="default" size="100%">Qiang Fu</style></author><author><style face="normal" font="default" size="100%">Florence Crombé</style></author><author><style face="normal" font="default" size="100%">Denis Piérard</style></author><author><style face="normal" font="default" size="100%">Kathleen Marchal</style></author><author><style face="normal" font="default" size="100%">Nancy Roosens</style></author><author><style face="normal" font="default" size="100%">Sigrid C.J. De Keersmaecker</style></author><author><style face="normal" font="default" size="100%">Kevin Vanneste</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods</style></title><secondary-title><style face="normal" font="default" size="100%">Microbial Genomics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Jan-03-2021</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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&amp;nbsp;Escherichia coli&amp;nbsp;(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&amp;nbsp;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&amp;nbsp;https://galaxy.sciensano.be.&amp;nbsp;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.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue></record></records></xml>