A5014816450- Genomics and Phylogenetic Studies
- Antimicrobial Resistance in Staphylococcus
- Antibiotic Resistance in Bacteria
- Bacterial Identification and Susceptibility Testing
- Pharmaceutical and Antibiotic Environmental Impacts
- Bacterial biofilms and quorum sensing
- Vector-borne infectious diseases
- RNA and protein synthesis mechanisms
- Evolution and Genetic Dynamics
- Antibiotic Use and Resistance
- Vibrio bacteria research studies
- Bacterial Infections and Vaccines
- Gut microbiota and health
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- Yersinia bacterium, plague, ectoparasites research
- Aquaculture disease management and microbiota
- Microbial Community Ecology and Physiology
- Insect symbiosis and bacterial influences
- Viral Infections and Vectors
- Pneumonia and Respiratory Infections
- Escherichia coli research studies
- Antibiotics Pharmacokinetics and Efficacy
- Plant Pathogenic Bacteria Studies
- Mycobacterium research and diagnosis
University of Bath
2016-2025
UK Health Security Agency
2023
University of Exeter
2019
The University of Melbourne
2018
Oxford University Clinical Research Unit
2018
Mahidol Oxford Tropical Medicine Research Unit
2016
Mahidol University
2016
Swansea University
2015
University of Oxford
1977-2004
John Radcliffe Hospital
2001-2004
Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence (MLST), which exploits unambiguous nature electronic portability nucleotide data microorganisms. evaluate MLST, determined sequences approximately 470-bp fragments from 11 housekeeping genes in a reference set 107 isolates Neisseria...
ABSTRACT The introduction of multilocus sequence typing (MLST) for the precise characterization isolates bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In fields, key prerequisite exploiting this resource is ability to discern relatedness patterns evolutionary descent among with similar genotypes. Traditional clustering techniques, such as dendrograms, provide very poor representation recent events, they attempt...
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-acquired infections that are becoming increasingly difficult to combat because emerging resistance all current antibiotic classes. The evolutionary origins MRSA poorly understood, no rational nomenclature exists, and there consensus on the number clones or relatedness described from different countries. We resolve these issues provide more thorough precise analysis evolution than has previously been possible....
Current methods for differentiating isolates of predominant lineages pathogenic bacteria often do not provide sufficient resolution to define precise relationships. Here, we describe a high-throughput genomics approach that provides high-resolution view the epidemiology and microevolution dominant strain methicillin-resistant Staphylococcus aureus (MRSA). This reveals global geographic structure within lineage, its intercontinental transmission through four decades, potential trace...
Staphylococcus aureus is an important nosocomial and community-acquired pathogen. Its genetic plasticity has facilitated the evolution of many virulent drug-resistant strains, presenting a major constantly changing clinical challenge. We sequenced approximately 2.8-Mbp genomes two disease-causing S. strains isolated from distinct settings: recent hospital-acquired representative epidemic methicillin-resistant EMRSA-16 clone (MRSA252), clinically globally prevalent lineage; invasive...
Insecticide resistance is one of the most widespread genetic changes caused by human activity, but we still understand little about origins and spread resistant alleles in global populations insects. Here, via microarray analysis all P450s Drosophila melanogaster , show that DDT-R a gene conferring to DDT, associated with overtranscription single cytochrome P450 gene, Cyp6g1 . Transgenic shows this alone both necessary sufficient for resistance. Resistance up-regulation are allele has...
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added generate hypotheses explore dynamics system under investigation. Selected static images then within publications highlight key findings wider audience. However, these very inadequate way exploring interpreting...
Staphylococcus aureus is an important human pathogen and represents a growing public health burden owing to the emergence spread of antibiotic-resistant clones, particularly within hospital environment. Despite this, basic questions about evolution population biology species, with regard extent impact homologous recombination, remain unanswered. We address these issues through analysis sequence data obtained from characterization by multilocus typing (MLST) 334 isolates S. aureus, recovered...
The identification of clones within bacterial populations is often taken as evidence for a low rate recombination, but the validity this inference rarely examined. We have used statistical tests congruence between gene trees to examine extent and significance recombination in six pathogens. For Neisseria meningitidis, Streptococcus pneumoniae, pyogenes, Staphylococcus aureus, maximum likelihood reconstructed using seven house-keeping genes was most cases no better than that each tree random...
Abstract Summary: The 32-bit Windows application START is implemented using Visual Basic and C++ performs analyses to aid in the investigation of bacterial population structure multilocus sequence data. These include data summary, lineage assignment, tests for recombination selection. Availability: available at http://outbreak.ceid.ox.ac.uk/software.htm. Contact: keith.jolley@ceid.ox.ac.uk * To whom correspondence should be addressed.
The widespread use of antibiotics in association with high-density clinical care has driven the emergence drug-resistant bacteria that are adapted to thrive hospitalized patients. Of particular concern globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clones cause outbreaks and epidemics associated health care. most rapidly spreading tenacious health-care-associated clone Europe currently is EMRSA-15, which was first detected UK early 1990s subsequently spread...
Background Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter into a database for further analysis. The recent introduction of mobile phones that utilise open source Android operating system, which include (among other features) both GPS Google Maps, provide new opportunities developing phone applications, conjunction with web allow two-way communication between workers project databases. Methodology Here we describe generic framework,...
Lyme borreliosis, caused by the tick-borne bacterium Borrelia burgdorferi, has become most common vector-borne disease in North America over last three decades. To understand dynamics of epizootic spread and to predict evolutionary trajectories B. accurate information on population structure relationships pathogen is crucial. We, therefore, developed a multilocus sequence typing (MLST) scheme for burgdorferi based eight chromosomal housekeeping genes. We validated MLST specimens from Europe,...
Generation time varies widely across organisms and is an important factor in the life cycle, history evolution of organisms. Although doubling (DT) has been estimated for many bacteria laboratory, it nearly impossible to directly measure natural environment. However, estimate can be obtained by measuring rate at which accumulate mutations per year wild they mutate generation laboratory. If we assume mutation same that all are neutral, assumption show not very important, then DT dividing...
Microbial virulence is a complex and often multifactorial phenotype, intricately linked to pathogen’s evolutionary trajectory. Toxicity, the ability destroy host cell membranes, adhesion, adhere human tissues, are major factors of many bacterial pathogens, including Staphylococcus aureus. Here, we assayed toxicity adhesiveness 90 MRSA (methicillin resistant S. aureus ) isolates found that while there was remarkably little variation in varied by over an order magnitude between isolates,...
ABSTRACT The implementation of routine whole-genome sequencing (WGS) promises to transform our ability monitor the emergence and spread bacterial pathogens. Here we combined WGS data from 308 invasive Staphylococcus aureus isolates corresponding a pan-European population snapshot, with epidemiological resistance data. Geospatial visualization is made possible by generic software tool designed for public health purposes that available at project URL (...
Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and genetic basis adaptation. Advances in whole genome sequencing technologies have led to a vast expansion amount genomes deposited public databases. There pressing need software solutions which are able cluster, catalogue characterise genes, or other features, increasingly large genomic datasets.Here we present pangenomics toolbox, PIRATE (Pangenome Iterative...
Abstract Chickens are the most common birds on Earth and colibacillosis is among diseases affecting them. This major threat to animal welfare safe sustainable food production difficult combat because etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address underlying evolutionary mechanisms of extraintestinal spread systemic infection poultry. Combining...
Abstract The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically ecologically diverse. Many species are opportunistic pathogens can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated pneumoniae clones that non-susceptible to carbapenems spread rapidly, representing a high public health burden. Here we report an analysis 3,482 genome sequences 15 sampled over 17-month period from wide range clinical, community,...