A5082557857- Genomics and Phylogenetic Studies
- Astronomy and Astrophysical Research
- Antibiotic Resistance in Bacteria
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Bacterial Identification and Susceptibility Testing
- Natural Language Processing Techniques
- Bacterial Genetics and Biotechnology
- Antimicrobial Resistance in Staphylococcus
- Crystallization and Solubility Studies
- Bacterial biofilms and quorum sensing
- X-ray Diffraction in Crystallography
- Radiomics and Machine Learning in Medical Imaging
- Plant Pathogenic Bacteria Studies
- Gene expression and cancer classification
- Legume Nitrogen Fixing Symbiosis
- Streptococcal Infections and Treatments
- Aquaculture disease management and microbiota
- Machine Learning in Bioinformatics
- Insect symbiosis and bacterial influences
- Pharmaceutical and Antibiotic Environmental Impacts
- Cystic Fibrosis Research Advances
- Genetic diversity and population structure
- Escherichia coli research studies
Justus-Liebig-Universität Gießen
2016-2025
German Center for Infection Research
2019-2024
Command-line annotation software tools have continuously gained popularity compared to centralized online services due the worldwide increase of sequenced bacterial genomes. However, results existing command-line pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference Here, we introduce Bakta, a new tool for robust, taxon-independent, thorough and, nonetheless, fast Bakta conducts comprehensive workflow including detection small proteins taking into...
Plasmids are extrachromosomal genetic elements that replicate independently of the chromosome and play a vital role in environmental adaptation bacteria. Due to potential mobilization or conjugation capabilities, plasmids important vehicles for antimicrobial resistance genes virulence factors with huge increasing clinical implications. They therefore subject large genomic studies within scientific community worldwide. As result rapidly improving next-generation sequencing methods, quantity...
Antimicrobial resistance (AMR) is one of the biggest global problems threatening human and animal health. Rapid accurate AMR diagnostic methods are thus very urgently needed. However, traditional antimicrobial susceptibility testing (AST) time-consuming, low throughput viable only for cultivable bacteria. Machine learning may pave way automated prediction based on genomic data comparing different machine encodings whole-genome sequencing without previously known knowledge remains to be...
Introduction: The increasing incidence of infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in sub-Saharan Africa is serious concern. Studies from countries with a highly industrialized poultry industry suggest the production-food-consumer chain as potential transmission route. In Africa, integrated studies at this human-animal interface are still missing. Aim: To determine molecular epidemiology ESBL-producing E. intestinal tract humans and rural Ghana....
Whole genome sequencing of bacteria has become daily routine in many fields. Advances DNA technologies and continuously dropping costs have resulted a tremendous increase the amounts available sequence data. However, comprehensive in-depth analysis resulting data remains an arduous time-consuming task. In order to keep pace with these promising but challenging developments transform raw into valuable information, standardized analyses scalable software tools are needed. Here, we introduce...
Abstract Purpose We designed and tested a point of care test panel to detect E.coli antibiotic susceptibility in urine samples from patients at the urological department. The aim this approach is facilitate choosing an appropriate for urinary tract infections (UTI) first presentation context increasing resistance uropathogens worldwide. Methods analyzed 162 isolates university department determine phenotypic genotypic data. With data we created customized LAMP (loop-mediated isothermal...
Motivation: The vast amount of already available and currently generated read mapping data requires comprehensive visualization, should benefit from bioinformatics tools offering a wide spectrum analysis functionality just one source. Appropriate handling multiple mapped reads during analyses remains an issue that demands improvement. Results: capabilities the visualization tool ReadXplorer were vastly enhanced. Here, we present even finer granulated classification, improving level detail...
The increase of Vancomycin-resistant Enterococcus faecium (VREfm) in recent years has been partially attributed to the rise specific clonal lineages, which have identified throughout Germany. To date, there is no gold standard for interpretation genomic data outbreak analyses. New approaches such as split k-mer analysis (SKA) could support cluster attribution routine investigation. aim this project was investigate frequent lineages VREfm during suspected outbreaks across different hospitals,...
Water is considered to play a role in the dissemination of antibiotic-resistant Gram-negative bacteria including those encoding Extended-spectrum beta-lactamases (ESBL) and carbapenemases. To investigate water for their spread more detail, we characterized ESBL/Carbapenemase-producing from surface sediment samples using phenotypic genotypic approaches. isolates were obtained water/sediment samples. Species antibiotic resistance determined. A subset these (n = 33) was whole-genome-sequenced...
Small regulatory RNAs (sRNAs) play a role in the control of bacterial virulence gene expression. In this study, we investigated an sRNA that was identified Streptococcus pyogenes (group A Streptococcus, GAS) but is conserved throughout various streptococci. deletion strain, expression mga, encoding multiple regulator, reduced. Accordingly, transcript and proteome analyses revealed decreased several Mga-activated genes. Therefore, because shown to interact with 5' UTR mga gel-shift assay,...
Abstract The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensive annotation with computational efficiency via alignment-free sequence identifications. However, usage software interpretation result files in various formats might be challenging pose technical barriers. Here, we present recent updates on web server, a user-friendly interface conducting visualizing annotations using without requiring...
The enormous success and ubiquitous application of next third generation sequencing has led to a large number available high-quality draft complete microbial genomes in the public databases.Today, NCBI RefSeq database release 90 alone contains 11,060 bacterial (Haft et al., 2018 ).Concurrently, selection appropriate reference (RGs) is increasingly important as it implications for routine in-silico analyses, example detection single nucleotide polymorphisms, scaffolding assemblies,...
ABSTRACT Plasmids are extrachromosomal genetic elements replicating independently of the chromosome which play a vital role in environmental adaptation bacteria. Due to potential mobilization or conjugation capabilities, plasmids important vehicles for antimicrobial resistance genes and virulence factors with huge increasing clinical implications. They therefore subject large genomic studies within scientific community worldwide. As result rapidly improving next generation sequencing...
Antimicrobial resistance (AMR) is a global health and development threat. In particular, multi-drug (MDR) increasingly common in pathogenic bacteria. It has become serious problem to public health, as MDR can lead the failure of treatment patients. typically result mutations accumulation multiple genes within single cell. Machine learning methods have wide range applications for AMR prediction. However, these approaches focus on drug prediction do not incorporate information accumulating...
Abstract Small proteins with fewer than 100, particularly 50, amino acids are still largely unexplored. Nonetheless, they represent an essential part of bacteria’s often neglected genetic repertoire. In recent years, the development ribosome profiling protocols has led to detection increasing number previously unknown small proteins. Despite this, overlooked in many cases by automated genome annotation pipelines, and often, no functional descriptions can be assigned due a lack known...
Antimicrobial resistance (AMR) has become one of the serious global health problems, threatening effective treatment a growing number infections. Machine learning and deep show great potential in rapid accurate AMR predictions. However, large samples for training these models is essential. In particular, novel antibiotics, limited data imbalance hinder models’ generalization performance overall accuracy. We propose transfer model that can improve prediction on small, imbalanced datasets. As...
Hospitals with their high antimicrobial selection pressure represent the presumably most important reservoir of multidrug-resistant human pathogens. Antibiotics administered in course treatment are excreted and discharged into wastewater system. Not only patients, but also sewers, substances exert on existing bacteria promote emergence dissemination clones. In previous studies, two main clusters were identified all sections hospital network that was investigated, one K. pneumoniae ST147...
Abstract Command line annotation software tools have continuously gained popularity compared to centralized online services due the worldwide increase of sequenced bacterial genomes. However, results existing command pipelines heavily depend on taxon specific databases or sufficiently well annotated reference Here, we introduce Bakta, a new tool for robust, taxon-independent, thorough and nonetheless fast Bakta conducts comprehensive workflow including detection small proteins taking into...
Abstract The Gram-stain-negative, oxidase negative, catalase positive strain KPC-SM-21 T , isolated from a digestate of storage tank mesophilic German biogas plant, was investigated by polyphasic taxonomic approach. Phylogenetic identification based on the nearly full-length 16S rRNA gene revealed highest sequence similarity to Acinetobacter baumannii ATCC 19606 (97.0%). trees calculated partial rpoB and gyrB sequences showed distinct clustering with gerneri DSM 14967 = CIP 107464 not A....
New polyketides, termed veramycins, were isolated along with their known congeners NFAT-133 and TM-123. Total synthesis from a central building block was accomplished, the BGC identified biosynthetic pathway for this molecule class proposed.
Abstract Increasing numbers of multi-drug resistant pathogens call for new chemical scaffolds, addressing novel targets, that can serve as lead structures the development life-saving drugs. For antibiotics, natural product-inspired molecules represent a most promising resource. Natural products evolved to high complexity and occupy space different than synthetic libraries. However, clinical translation is often impeded by their relative inaccessibility medicinal chemistry optimization, e.g....
Abstract Several species of the Gram-negative genus Bordetella are cause respiratory infections in mammals and birds, including whooping cough (pertussis) humans. Very recently, a novel atypical species, pseudohinzii , was isolated from laboratory mice. These mice presented no obvious clinical symptoms but elevated numbers neutrophils bronchoalveolar lavage fluid inflammatory signs histopathology. We noted that this can occur at high prevalence mouse facility despite regular pathogen testing...
Enterobacter bugandensis is the most pathogenic species of genus and a cause life-threatening infections in neonates. Curiously, it was also detected samples from International Space Station. Here, we present complete closed genome sequences two clinical E. isolates recognized for first time Germany.
Staphylococcus capitis naturally colonizes the human skin but as an opportunistic pathogen, it can also cause biofilm-associated infections and bloodstream in newborns. Previously, we found that two strains from subspecies S. subsp. produce yellow carotenoids despite initial species description, reporting this non-pigmented. In aureus, golden pigment staphyloxanthin is important virulence factor, protecting cells against reactive oxygen modulating membrane fluidity. study, used pigmented...