A5036834740- Antibiotic Resistance in Bacteria
- Escherichia coli research studies
- Pharmaceutical and Antibiotic Environmental Impacts
- Vibrio bacteria research studies
- Probiotics and Fermented Foods
- Bacterial Identification and Susceptibility Testing
- Enterobacteriaceae and Cronobacter Research
- Microbial Metabolites in Food Biotechnology
- Bacterial biofilms and quorum sensing
- Infections and bacterial resistance
- Genomics and Phylogenetic Studies
- Mycobacterium research and diagnosis
- Salmonella and Campylobacter epidemiology
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Yersinia bacterium, plague, ectoparasites research
- Antibiotics Pharmacokinetics and Efficacy
- Bacteriophages and microbial interactions
- Gut microbiota and health
Central European Institute of Technology
2019-2024
Vrije Universiteit Brussel
2022
VIB-VUB Center for Structural Biology
2022
Vlaams Instituut voor Biotechnologie
2022
University of Veterinary Sciences Brno
2019-2022
Abstract Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. (ExPEC), which belong phylogroup B2, belongs the environmental/commensal B1. Here, we present pan-genomic analysis of global collection 752 isolates from diverse sources. We identify large sub-lineage characterized by near ubiquitous carriage ColV plasmids, carry genes encoding virulence factors, and distinct accessory...
Introduction Hospitals and wastewater are recognized hot spots for the selection dissemination of antibiotic-resistant bacteria to environment, but total participation hospitals in spread nosocomial pathogens municipal treatment plants (WWTPs) adjacent rivers had not previously been revealed. Methods We used a combination culturing whole-genome sequencing explore transmission routes Escherichia coli from hospitalized patients suffering urinary tract infections (UTI) via environment. Samples...
By compiling various genomic and phenotypic data sets, we have provided one of the most comprehensive studies Escherichia coli isolates from Australian silver gull, on media containing clinically relevant antibiotics. The analysis genetic structures capturing antimicrobial resistance genes across three gull breeding colonies in New South Wales, Australia, comparisons to clinical revealed a range trackable signatures that highlight broad distribution more than 170 different lineages E. .
Silver gulls carry phylogenetically diverse Escherichia coli, including globally dominant extraintestinal pathogenic E. coli (ExPEC) sequence types and pandemic ExPEC-ST131 clades; however, our large-scale study (504 samples) on silver nesting off the coast of New South Wales identified ST457 as most prevalent. A phylogenetic analysis whole-genome sequences (WGS) 138 samples comprising 42 from gulls, 2 humans (Australia), 14 poultry farmed in Paraguay were compared with 80 WGS deposited...
Acinetobacter baumannii is an opportunistic pathogenic bacterium prioritized by WHO and CDC because of its increasing antibiotic resistance. Heterogeneity among strains represents the hallmark A. bacteria. We wondered to what extent extensively used strains, so-called reference reflect dynamic nature intrinsic heterogeneity these analyzed multiple phenotypic traits 43 nonredundant, modern, multidrug-resistant, drug-resistant, pandrug-resistant clinical isolates broadly baumannii. Comparison...
The occurrence of colistin resistance has increased rapidly among Enterobacterales around the world. We performed a national survey plasmid-mediated in human clinical isolates through retrospective analysis samples from 2009 to 2017 and prospective sampling 2018–2020. aim this study was identify characterize with mcr genes various regions Czech Republic using whole genome sequencing (WGS). Of all 1932 colistin-resistant analyzed, 73 (3.8%) were positive for genes. Most carried mcr-1 (48/73)...
In this study, we characterize a new collection that comprises multidrug-resistant (MDR), extensively drug-resistant (XDR), pandrug-resistant (PDR), and carbapenem-resistant modern clinical isolates of Acinetobacter baumannii collected from hospitals through national microbiological surveillance in Belgium. Bacterial (n = 43) were subjected to whole-genome sequencing (WGS), combining Illumina (MiSeq) Nanopore (MinION) technologies, which high-quality genomes (chromosome plasmids) de novo...
ABSTRACT The aim of this study was to determine the occurrence plasmid-mediated colistin resistance in domestic and imported meat slaughter animals Czech Republic during 2020–2021 by using selective cultivation direct PCR testing. A total 111 colistin-resistant Escherichia coli isolates with mcr-1 gene were obtained from 65 (9.9%, n = 659) samples subjected whole-genome sequencing. Isolates mcr frequently found fresh production (14.2%) as well import (28.8%). -positive E. predominantly...
The type VI secretion system (T6SS) is a versatile nanomachine that injects effectors into target cells, playing role in bacterial competition and virulence. While widespread Gram-negative bacteria, T6SS prevalence varies across species strains, its distribution Escherichia coli remains underexplored despite E. being an important intestinal (IPEC) extraintestinal (ExPEC) pathogen. Here, we examined the of subclasses (T6SS i ) 131610 genomes, which annotated for clinical relevance. genes were...
Phenotypic outcomes can be heavily affected by environmental factors. In this study, we exploited the previously observed nutrient-dependency of cell biological phenotypic features, captured a cross-condition image-based profiling assay Escherichia coli deletion strains, to examine in more detail. We identified several general principles, including existence spectrum deviating phenotypes across nutrient conditions (i.e., from nutrient- or feature-specific pleiotropic deviations), limited...
Abstract Acinetobacter baumannii is a critical, opportunistic pathogen due to its multi- pandrug-resistance including resistance last-resort antibiotics such as carbapenems. While A. can acquire environmental DNA through multiple mechanisms natural competence, one of the most common acquisition via plasmids by conjugation. One challenges for conjugation an active Type VI Secretion System (T6SS), which kills nonkin bacteria and therefore inhibits The genes has helped spread resistant clones...
This study is focused on Escherichia spp. isolates resistant to critically important antibiotics (cefotaxime, ciprofloxacin and colistin) among Caspian gull's (Larus cachinnans) chicks nesting in the Nove Mlyny Water Reservoir, Czech Republic. The prevalence of antimicrobial resistance (AMR) bacteria within wild birds commonly evaluated using a single sampling event, capturing only brief momentary snapshot at particular location. Therefore, gulls our were sampled May 2018 (n = 72) 2019 45),...
Poultry represents a common source of bacteria with resistance to antibiotics including the critically important ones. Selective cultivation using colistin, cefotaxime and meropenem was performed for 66 chicken samples coming from 12 farms in Paraguay while two breeding companies supplied farms. A total 62 Escherichia coli 22 Klebsiella pneumoniae isolates were obtained representative subjected whole-genome sequencing. Relatively high prevalence phylogenetic group D F observed E. several...
The relatedness of the equine-associated Escherichia coli ST1250 and its single- double-locus variants (ST1250-SLV/DLV), obtained from horses in Europe, was studied by comparative genome analysis. A total 54 isolates E. ST1250-SLV/DLV healthy hospitalized across Europe [Czech Republic (n=23), Netherlands (n=18), Germany (n=9), Denmark (n=3) France (n=1)] 2008-2017 were subjected to whole-genome sequencing. An additional 25 draft assemblies public databases. compared for genomic features,...
Abstract We assembled the whole genome sequence (WGS) of a collection 43 non-redundant modern clinical isolates and four broadly used reference strains Acinetobacter baumannii . Comparison these their WGS confirmed high heterogeneity in capsule loci, types, presence virulence antibiotic resistance genes. However, significant portion strongly differ when compared to several light colony morphology, cellular density, production, natural transformability vivo virulence. These genetic phenotypic...
Abstract The occurrence of colistin resistance has increased rapidly among Enterobacterales around the world. We performed a national survey plasmid-mediated in human clinical isolates by retrospective analysis samples from 2009-2017 and prospective sampling 2018-2020. aim this study was to identify characterize with mcr genes various regions Czech Republic using whole genome sequencing (WGS). Of all 1932 colistin-resistant analyzed, 73 (3.8%) were positive for genes. Most carried mcr-1...
It was believed that members of the family Enterobacteriaceae are unable to grow under conditions with short-chain fructooligosaccharides as only source carbon. Nevertheless, first Escherichia coli isolate from chicken intestine able utilize these sugars owing chromosomally harbored fos operon.