PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in .

Accurate reconstruction of antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct plasmids using short reads. We developed plasmidEC, an ensemble classifier that identifies plasmid-derived contigs by combining the output of three different binary classification tools.

Integrated surveillance of human respiratory viruses in addition to SARS-CoV-2 in a public testing facility in the Netherlands.

Background: SARS-CoV-2 prevention measures impact the circulation of other respiratory viruses. Surveillance in the network of general practitioners is hampered by widespread testing for SARS-CoV-2 in public testing facilities.

Objectives: To evaluate integrated community surveillance of SARS-CoV-2 and other respiratory viruses and describe epidemiological trends.

Recovering Plasmids in the Absence of Long-Read Sequencing Data.

The incidence of infections caused by multidrug-resistant strains has risen in the past years. Antibiotic resistance in is often mediated by acquisition and maintenance of plasmids. The study of plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed.

as a cause for prosthetic valve endocarditis and post-sternotomy mediastinitis.

An otherwise healthy patient, with minimal clinical, biochemical and peroperative signs of infection, was diagnosed with prosthetic valve endocarditis by 16S PCR. The patient subsequently developed a post-sternotomy mediastinitis and was the only detected pathogen. can cause severe infections in individuals not classically at risk, and may be missed in the routine diagnostic work-up of endocarditis.