W. van Schaik

A novel resistance reversion mechanism in a vancomycin-variable Enterococcus faecium strain

The paper identifies a vancomycin-variable Enterococcus faecium isolate that reverts to resistance via a novel mechanism involving vanHAX gene activation through genomic rearrangements.

Growth in a biofilm promotes conjugation of a blaNDM-1-bearing plasmid between Klebsiella pneumoniae strains

This study shows biofilm growth significantly increases conjugative transfer of a carbapenem resistance plasmid in K. pneumoniae without fitness costs.

Extended-spectrum beta-lactamase genes traverse the Escherichia coli populations of ICU patients, staff and environment.

This study tracks the spread of ESBL-EC in an ICU, finding distinct patient and environmental isolates but shared plasmid lineages carrying blaCTX-M genes.

Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts

This study improves noise reduction in metagenomic chromosome conformation capture to link antibiotic resistance genes to their microbial hosts in the human gut microbiome.

Colistin resistance mutations in phoQ sensitize Klebsiella pneumoniae to IgM-mediated complement killing

This study shows that colistin resistance mutations in K. pneumoniae increase sensitivity to IgM-mediated complement killing via PhoQ activation.

GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes

This study characterizes GR13 plasmids in Acinetobacter, showing their capacity to accumulate and horizontally transfer diverse accessory genes through dif modules and insertion sequences.

Gauge your phage: Benchmarking of bacteriophage identification tools in metagenomic sequencing data

This study benchmarks ten phage identification tools on metagenomic data, finding VirSorter2 and Kraken2 perform best, with false positives and diversity bias noted.

Microbiota analysis of rural and urban surface waters and sediments in Bangladesh identifies human waste as driver of antibiotic resistance

The paper analyzes antibiotic resistance genes in surface waters and sediments from rural and urban areas in Bangladesh, finding that urban areas have higher levels of resistance genes linked to human gut bacteria.

Microevolution of acquired colistin resistance in Enterobacteriaceae from ICU patients receiving selective decontamination of the digestive tract.

This study identifies mechanisms of acquired colistin resistance in Enterobacteriaceae from ICU patients on SDD, revealing novel variants and highlighting resistance emergence during prophylactic use.

In vitro evolution of colistin resistance in the Klebsiella pneumoniae complex follows multiple evolutionary trajectories with variable effects on fitness and virulence characteristics.

This study shows that Klebsiella pneumoniae complex strains can develop colistin resistance through multiple evolutionary paths, with variable effects on fitness and virulence.

Conditionally essential genes for survival during starvation in Enterococcus faecium E745

This study identifies genes essential for Enterococcus faecium survival during starvation using Tn-seq, highlighting usp as a key gene for environmental robustness.

CRISPR-Cas9 mediated genome editing in vancomycin resistant Enterococcus faecium

This paper describes a CRISPR-Cas9 method to efficiently generate targeted mutants in E. faecium, reducing the time from 4-5 weeks to 3 weeks.

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

This study examines changes in gut microbiota diversity and pathogen presence in ICU patients, finding reduced diversity and pathogen domination linked to antimicrobial use.

Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization

This study analyzes genome dynamics of Enterococcus faecium during long-term asymptomatic gut colonization in patients, revealing high genomic flexibility and horizontal gene transfer.

On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data

This study evaluates plasmid reconstruction algorithms from short-read sequencing data using reference genomes, finding that none fully and unambiguously predict plasmid sequences, with performance varying by plasmid size and assembly quality.

In-Depth Resistome Analysis by Targeted Metagenomics

The paper introduces ResCap, a targeted metagenomics platform for analyzing resistomes, enhancing sensitivity and specificity in detecting antimicrobial resistance genes.

Gut microbiota and resistome dynamics in intensive care patients receiving selective digestive tract decontamination

This study examines gut microbiota and resistome changes in ICU patients undergoing selective decontamination, finding reduced diversity and specific resistance gene abundance.

Fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum

This study identifies genes essential for vancomycin-resistant Enterococcus faecium growth in human serum and their role in virulence.