Background With the efficiency and the decreasing cost of next-generation sequencing, the
technology is being rapidly introduced into clinical and public health laboratory practice …

Background Whole genome sequence (WGS)-based strain typing finds increasing use in the
epidemiologic analysis of bacterial pathogens in both public health as well as more …

SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of
microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit …

Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient
populations in hospitals around the world. Intensive care unit (ICU) patients are particularly …

Abstract Next Generation Sequencing (NGS) combined with powerful bioinformatic
approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of …

Whole-genome sequencing (WGS) is increasingly used by food regulatory and public health
agencies in the United States to facilitate the detection, investigation, and control of …

This multiagency report developed by the Interagency Collaboration for Genomics for Food
and Feed Safety provides an overview of the use of and transition to whole genome …

There is growing interest in reconstructing phylogenies from the copious amounts of
genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To …

The recent widespread application of whole-genome sequencing (WGS) for microbial
disease investigations has spurred the development of new bioinformatics tools, including a …

The Bacillus cereus group comprises multiple species capable of causing emetic or
diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses …