A5077243236- Antibiotic Resistance in Bacteria
- Bacterial Identification and Susceptibility Testing
- Antimicrobial Resistance in Staphylococcus
- Genomics and Phylogenetic Studies
- Bacterial biofilms and quorum sensing
- Vibrio bacteria research studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Yersinia bacterium, plague, ectoparasites research
- Antibiotics Pharmacokinetics and Efficacy
- Escherichia coli research studies
- Infective Endocarditis Diagnosis and Management
- Infections and bacterial resistance
- Bacillus and Francisella bacterial research
- Systemic Lupus Erythematosus Research
- Antibiotic Use and Resistance
- HIV Research and Treatment
- Cytomegalovirus and herpesvirus research
- Enterobacteriaceae and Cronobacter Research
- Monoclonal and Polyclonal Antibodies Research
- Gut microbiota and health
- Immune Cell Function and Interaction
- Zoonotic diseases and public health
- Molecular Biology Techniques and Applications
- Mycobacterium research and diagnosis
University of Freiburg
2017-2025
University Medical Center Freiburg
2017-2025
European Society of Clinical Microbiology and Infectious Diseases
2024
University of Education Freiburg
2024
Institute of Medical Microbiology and Hygiene
2021-2023
Wellcome Sanger Institute
2012-2019
Genomics (United Kingdom)
2014-2019
University of Cambridge
2015-2019
Addenbrooke's Hospital
2016-2019
CS Diagnostics
2018
Abstract Summary: A typical prokaryote population sequencing study can now consist of hundreds or thousands isolates. Interrogating these datasets provide detailed insights into the genetic structure prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying core and accessory genes. Roary makes construction genome samples possible on standard desktop without compromising accuracy results. Using single CPU produce consisting 1000 isolates in 4.5...
The genus Legionella comprises 65 species, among which pneumophila is a human pathogen causing severe pneumonia. To understand the evolution of an environmental to accidental pathogen, we have functionally analyzed 80 genomes spanning 58 species. Uniquely, immense repository 18,000 secreted proteins encoding 137 different eukaryotic-like domains and over 200 paired with highly conserved type IV secretion system (T4SS). Specifically, show that eukaryotic Rho- Rab-GTPase are found nearly...
ABSTRACT To give an update on the molecular epidemiology and global distribution of carbapenemase encoding genes, we subjected 313 carbapenem-resistant Acinetobacter baumannii isolated from 114 study centers in 47 countries five world regions, Africa, Asia, Europe, Latin America, North to whole genome sequencing. Numbers isolates investigated were proportional population size contributing countries. Molecular was using seven-loci core multilocus sequence typing, whole-genome single...
Abstract Carbapenem-resistant Klebsiella pneumoniae (CRKP) are of particular concern due to the spread antibiotic resistance genes associated with mobile genetic elements. In this study, we collected 687 carbapenem-resistant strains recovered among clinical samples from 41 hospitals in nine Southern European countries (2016-2018). We identified 11 major clonal lineages, most isolates belonging high-risk clones ST258/512, ST101, ST11, and ST307. bla KPC-like was prevalent...
<h3>Importance</h3> The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range bacteria in less than day. These could be used to more effectively contain the spread multidrug-resistant pathogens. <h3>Objective</h3> To compare WGS with standard clinical microbiology practice investigation nosocomial outbreaks caused by bacteria, identification genetic determinants antimicrobial resistance, and typing other clinically...
Significance Our past understanding of pathogen evolution has been fragmented because tendencies to study human clinical isolates. To understand the evolutionary trends pathogenic bacteria though, we need context their nonpathogenic relatives. unique and detailed dataset allows description parallel two key pathogens: causative agents plague Yersinia diarrhea. The analysis reveals an emerging pattern where few virulence-related functions are found in all lineages, representing “foothold”...
ABSTRACT Summary A typical prokaryote population sequencing study can now consist of hundreds or thousands isolates. Interrogating these datasets provide detailed insights into the genetic structure prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying core and dispensable accessory genes. Roary makes construction genome samples possible on standard desktop without compromising accuracy results. Using single CPU produce consisting 1000...
Significance In many clinically important bacteria, antibiotic resistance genes are primarily carried on plasmids. These can spread horizontally between different strains and species. However, current surveillance systems track chromosomal lineages of bacteria only, leading to an incomplete understanding how spreads, from within individual hospital across country borders. We present integrated, high-resolution analysis both chromosome plasmid sequences using Klebsiella pneumoniae isolates...
Longitudinal genomic and epidemiological surveillance of methicillin-resistant Staphylococcus aureus in the UK reveals extensive transmission hospitals community.
Objectives Epidemiological investigations of Legionnaires’ disease outbreaks rely on the rapid identification and typing clinical environmental Legionella isolates in order to identify control source infection. Rapid bacterial whole-genome sequencing (WGS) is an emerging technology that has potential rapidly discriminate outbreak from non-outbreak a clinically relevant time frame. Methods We performed pilot study determine feasibility using WGS differentiate collected during disease. Seven...
Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) 495 E. bloodstream isolates from 2001–2011 in the United Kingdom and Ireland (UK&I) 11 a reference collection. Comparison between WGS multilocus sequence typing (MLST) identified major discrepancies for 17% isolates, with multiple instances same type (ST) being located genetically distant positions tree. This confirms that...
Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. We conducted a survey of extended β-lactamase (ESBL)-producing E. isolated patients, canals and livestock wastewater eastern Thailand between 2014 2015, analyzed isolates using whole genome sequencing. The bacterial collection 149 consisted 84 single hospital 65 the sewer, farm within 20 km radius. ST131 predominated clinical...
Vancomycin-resistant Enterococcus faecium (VREfm) is a leading cause of nosocomial infection. Here, we describe the utility whole-genome sequencing in defining VREfm transmission.
Acquisition of multiple carbapenemase genes by Klebsiella pneumoniae (Kp) is an emerging public health threat. Here, we aim to elucidate the population structure Kp blood isolates carrying two different and identify mechanism facilitating their dissemination. The study was conducted in a tertiary healthcare center between 2014 2022. Twenty-four patients with bacteremia caused were identified. All 24 analyzed short-read genome sequences supplemented long reads selected number isolates....
ObjectivesGenome sequencing will be increasingly used in the clinical setting to tailor antimicrobial prescribing and inform infection control outbreaks. A recent technological innovation that could reduce delay between pathogen sampling data generation is single molecule sequencing. An example of this technology, which undergoing evaluation through an early access programme, Oxford Nanopore MinION.
<h3>Background</h3> Spondyloarthritis (SpA) is a common debilitating inflammatory disorder. Establishing the diagnosis often difficult, since abnormalities in conventional X-ray develop with latency of several years and only HLA-B27 used as laboratory marker. The goal our study was to identify new autoantibodies diagnostic markers SpA. <h3>Methods</h3> Protein array technology screen for autoantigens ankylosing spondylitis. Then, results were confirmed by ELISA using Class II-associated...
Background: Bacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrugresistant organisms and transmission these pathogens across healthcare networks.We used WGS define vancomycin-resistant enterococci (VRE) within a long-term care facility (LTCF), between this an acute hospital in United Kingdom (UK).Methods: A longitudinal prospective observational study faecal VRE carriage was conducted LTCF Cambridge, UK.Stool samples were collected at recruitment, then...
Two Southeast Asian students attending the same school in United Kingdom presented with pulmonary tuberculosis. An epidemiological investigation failed to link two cases, and drug resistance profiles of Mycobacterium tuberculosis isolates were discrepant. Whole-genome sequencing found them be genetically identical, suggesting a missed transmission event.
The correct interpretation of microbial sequencing data applied to surveillance and outbreak investigation depends on accessible genomic databases provide vital genetic context. Our aim was construct describe a United Kingdom MRSA database containing over 1000 methicillin-resistant Staphylococcus aureus (MRSA) genomes drawn from England, Northern Ireland, Wales, Scotland, the Republic Ireland decade. We sequenced 1013 submitted British Society for Antimicrobial Chemotherapy by 46...