A5004742977- Antifungal resistance and susceptibility
- Mycobacterium research and diagnosis
- Bacterial Identification and Susceptibility Testing
- Antibiotic Resistance in Bacteria
- Antimicrobial Resistance in Staphylococcus
- Infectious Diseases and Mycology
- Tuberculosis Research and Epidemiology
- Pneumonia and Respiratory Infections
- Fungal Biology and Applications
- Helminth infection and control
- Streptococcal Infections and Treatments
- Infective Endocarditis Diagnosis and Management
- Microbial Natural Products and Biosynthesis
- SARS-CoV-2 and COVID-19 Research
- Antibiotics Pharmacokinetics and Efficacy
- Fungal Infections and Studies
- Bacteriophages and microbial interactions
- SARS-CoV-2 detection and testing
- Plant Pathogens and Fungal Diseases
- Molecular Biology Techniques and Applications
- Neonatal and Maternal Infections
- Malaria Research and Control
- Mycotoxins in Agriculture and Food
- Vibrio bacteria research studies
- Genomics and Phylogenetic Studies
Radboud University Nijmegen
2017-2024
Radboud University Medical Center
2017-2024
MSD (Netherlands)
2024
Radboud Institute for Molecular Life Sciences
2021-2023
University Medical Center
2018-2021
Netherlands Organisation for Applied Scientific Research
2013
In this study, we collected water from different locations in 32 drinking distribution networks the Netherlands and analysed spatial temporal variation microbial community composition by high-throughput sequencing of 16S rRNA gene amplicons. We observed that compositions raw source processed were very for each network sampled. network, major differences between water, although structures did not differ substantially end-point tap water. End-point samples within same revealed similar...
<h3>Importance</h3> Resistance of gram-negative bacilli to carbapenems is rapidly emerging worldwide. In 2016, the World Health Organization defined hospital-built environment as a core component infection prevention and control programs. The has recently been reported source for outbreaks sporadic transmission events carbapenemase-producing from patients. <h3>Objective</h3> To assess risk after identification an unexpected, severe, lethal hospital-acquired caused by...
Whole genome sequencing (WGS) is widely used for outbreak analysis of bacteriology and virology but scarcely in mycology. Here, we WGS genotyping
Aspergillus fumigatus is a saprophytic fungus that extensively produces conidia. These microscopic asexually reproductive structures are small enough to reach the lungs. Germination of conidia followed by hyphal growth inside human lungs key step in establishment infection immunocompromised patients. RNA-Seq was used analyze transcriptome dormant and germinating A. Construction gene co-expression network revealed four clusters (modules) correlated with phase (dormant, isotropic growth,...
The prevalence of azole resistance in clinical and environmental Aspergillus fumigatus isolates is rising over the past decades, but molecular basis development antifungal drug not well understood. This study focuses on role phenotypic plasticity evolution A. fumigatus. When challenged with a new stressful environment, may allow to adjust their physiology still enable growth reproduction, therefore allowing establishment genetic adaptations through natural selection available variation...
Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by antimalarial drugs. Most mitochondrial proteins are imported into this organelle, our picture of the proteome remains incomplete. Many data sources contain information about localization, including gene expression profiles, orthology to from other species, coevolutionary relationships, amino acid sequences, each with different coverage reliability. To obtain...
During the course of SARS-CoV-2 pandemic reports mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations hospitals in monitoring transmission rising levels mutant strains. Here we report a novel WGS technique for SARS-CoV-2, EasySeq™ RC-PCR kit. By applying reverse complement polymerase chain reaction (RC-PCR), an Illumina library...
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic Molecular Diagnostics (ESGMD) Swiss (SSM), aims to build a framework between laboratories in order improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out 15 clinical that had free choice...
ABSTRACT Germination of inhaled Aspergillus fumigatus conidia is a necessary sequitur for infection. starts with the breaking dormancy, which initiated by an increase cellular perimeter in process termed isotropic growth. This swelling phase followed polarized growth, resulting formation germ tube. The multinucleate tubular cells exhibit tip growth from hyphae, after lateral branches emerge to form mycelial network. regulatory mechanisms governing conidial germination are not well defined....
AmpC-β-lactamase production is an under-recognized antibiotic resistance mechanism that renders Gram-negative bacteria resistant to common β-lactam antibiotics, similar the well-known ESBLs. For infection control purposes, it important be able discriminate between plasmid-mediated AmpC (pAmpC) and chromosomal-mediated (cAmpC) hyperproduction in as pAmpC requires isolation precautions minimize risk of horizontal gene transmission. Detecting Escherichia coli challenging, both cAmpC may lead...
Mycobacterium abscessus is an opportunistic pathogen notorious for its resistance to most classes of antibiotics and low cure rates. M. carries array mostly unexplored defense mechanisms. A deeper understanding antibiotic tolerance mechanisms pivotal in development targeted therapeutic regimens. We provide the first description all major transcriptional recommended current guidelines, using RNA sequencing-guided experiments. ATCC 19977 bacteria were subjected subinhibitory concentrations...
The opportunistic pathogen Aspergillus fumigatus is found on all continents and thrives in soil agricultural environments. Its ability to readily adapt novel environments produce billions of spores led the spread azole-resistant A. across globe, posing a threat many immunocompromised patients, including critically ill patients with severe influenza or COVID-19. In our study, we sought compare adaptational response azoles from isolates that differ azole susceptibility genetic background. To...
In 2015 and 2016, two Barramundi (Lates calcarifer) farms in Singapore reported a disease outbreak characterized by lethargic behavior, pronounced inappetence, generalized skin lesions, erosions of the fins tail, ultimately high mortality their fish. Next-generation sequencing PCR confirmed presence novel virus belonging to Alloherpesviridae family, Lates calcarifer herpesvirus (LCHV), which was subsequently isolated cultured. We characterize, for first time, complete genome cultured LCHV...
Abstract We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly MSSA carriage surveillance and cross-sectional screenings of health workers (HCWs) were available for outbreak tracing. Traditional clustering isolates by spa typing Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. investigated whether whole-genome sequencing...
Whole-genome sequencing is becoming the de facto standard for bacterial outbreak surveillance and infection prevention. This accompanied by a variety of bioinformatic tools needs bioinformatics expertise implementation. However, little known about concordance reported outbreaks when using different workflows. In this multi-centre proficiency testing among 13 major Dutch healthcare-affiliated centres, whole-genome analysis was assessed. Centres who participated obtained two randomized...
Currently, nontuberculous mycobacteria (NTM) are identified using small genomic regions, and species-level identification is often not possible. We introduce a next-generation sequencing (NGS) workflow that identifies to (sub)species level on the basis of whole genome extracted from enriched shotgun metagenomic data.
Staphylococcus aureus decolonization has proven successful in prevention of S. infections and is a key strategy to maintain venous access avoid hospitalization patients receiving home parenteral nutrition (HPN). We aimed determine the most effective safe long-term regimen.A randomized, open-label, multicenter clinical trial was conducted. Adult intestinal failure with HPN support carrying were randomly assigned 'continuous suppression' (CS) strategy, repeated chronic topical antibiotic...
The identification of the causative infectious pathogen in patients suspected having a bacterial infection is essential for diagnosis and start appropriate treatment. Over past 2 decades, molecular diagnostics have improved ability to detect identify bacteria.
ABSTRACT Phase-variable type I restriction modification (RM) systems are epigenetic regulatory that have been identified in numerous human bacterial pathogens. We previously showed an emerging zoonotic lineage of Streptococcus suis acquired a phase-variable RM system, named SsuCC20p. The SsuCC20p locus was the genome multiple streptococcal species, indicating it is not restricted to S. and can be through horizontal gene transfer. demonstrate phase variability relies on recombinase present...
Cefotaxime (CTX) is a third-generation cephalosporin (3GC) commonly used to treat infections caused by Escherichia coli. Two genetic mechanisms have been associated with 3GC resistance in E. The first the conjugative transfer of plasmid harbouring antibiotic-resistance genes. second introduction mutations promoter region ampC β-lactamase gene that cause chromosome-encoded hyperproduction. A wide variety related AmpC hyperproduction described. However, their link CTX has not reported. We...
Mycobacterium avium (M. avium) complex bacteria cause opportunistic infections in humans. Treatment yields cure rates of 60% and consists a macrolide, rifamycin, ethambutol, severe cases, amikacin. Mechanisms antibiotic tolerance remain mostly unknown. Therefore, we studied the contribution efflux amikacin modification to susceptibility.We characterised M. ABC transporters their expression together with other following exposure clarithromycin, amikacin, rifampicin. We determined effect...