Current methods struggle to reconstruct and visualize the genomic relationships of large
numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic …

High-throughput sequencing methods generated allele and single nucleotide polymorphism
information for thousands of bacterial strains that are publicly available in online …

Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology
and outbreak detection. However, there is a lack of open-source scalable software for …

In response to the EFSA call New approaches in identifying and characterizing microbial
and chemical hazards, the project INNUENDO ( https://sites.google.com/site/theinnuendoproject…

Background Presently, the bottleneck in the deployment of high-throughput sequencing
technology is the ability to analyse the increasing amount of data produced in a fit-for-purpose …

We characterised Lancefield group B streptococcal (GBS) isolates causing invasive disease
among non-pregnant adults in Portugal between 2009 and 2015. All isolates (n = 555) were …

Background Polymorphic toxins (PTs) are multi-domain bacterial exotoxins belonging to
distinct families that share common features in terms of domain organization. PTs are found in …

One Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, and coccobacilli-shaped
strain, designated c10Ua161M T , was isolated from a urine sample from a …

Background The rise of antibiotic resistance in pathogenic bacteria is a significant problem
for the treatment of infectious diseases. Resistance is usually selected by the antibiotic itself; …

Background The de novo assembly of raw sequence data is key in metagenomic analysis. It
allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences …