Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive
approach for pathogen detection. The cost of high-throughput or next-generation …

As a leading cause of bacterial dysentery, Shigella represents a significant threat to public
health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) …

Metagenomic characterization of microbial communities has the potential to become a tool
to identify pathogens in human samples. However, software tools able to extract strain-level …

Emerging next-generation sequencing technologies have revolutionized the collection of
genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings …

Background In this study, we aimed to perform a comprehensive analysis on the
metagenomic next-generation sequencing for the etiological diagnosis of septic patients …

An increasing amount of species and gene identification studies rely on the use of next
generation sequence analysis of either single isolate or metagenomics samples. Several …

Background Bloodstream infections remain one of the major challenges in intensive care
units, leading to sepsis or even septic shock in many cases. Due to the lack of timely …

Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not
rapid enough for real-time disease surveillance and do not give a quantitative picture of …

Numerous studies are currently underway to characterize the microbial communities
inhabiting our world. These studies aim to dramatically expand our understanding of the …

Background In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic
Escherichia coli O104: H4. The large amount of samples sent to microbiology laboratories …