David M. Aanensen
A5068117269- Antibiotic Resistance in Bacteria
- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Antimicrobial Resistance in Staphylococcus
- Pneumonia and Respiratory Infections
- SARS-CoV-2 and COVID-19 Research
- Vibrio bacteria research studies
- Salmonella and Campylobacter epidemiology
- Bacterial Infections and Vaccines
- Bacterial biofilms and quorum sensing
- Antibiotic Use and Resistance
- Bacteriophages and microbial interactions
- Reproductive tract infections research
- Antibiotics Pharmacokinetics and Efficacy
- Antifungal resistance and susceptibility
- COVID-19 epidemiological studies
- Streptococcal Infections and Treatments
- SARS-CoV-2 detection and testing
- Fungal Infections and Studies
- Probiotics and Fermented Foods
- Plant Pathogenic Bacteria Studies
- Global Maternal and Child Health
- Syphilis Diagnosis and Treatment
- Escherichia coli research studies
- Gut microbiota and health
Open Data Institute
2020-2024
University of Oxford
2018-2024
Science Oxford
2024
Wellcome Sanger Institute
2014-2023
The University of Queensland
2023
International Centre for Diarrhoeal Disease Research
2023
Imperial College London
2012-2022
Centre for Human Genetics
2016-2022
Quadram Institute
2022
UK Research and Innovation
2021
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...
Abstract The response of the global virus genomics community to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards ‘real-time’ generation and sharing SARS-CoV-2 genomic data. rapid growth in genome data production necessitated development new analytical methods that can deal orders magnitude more genomes than previously available. Here, we present describe Phylogenetic Assignment Named Global Outbreak Lineages...
Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive a selective advantage but may also be due to random founder effect. We investigate hypothesis for positive selection in United Kingdom using more than 25,000 whole genome sequences. Despite availability large dataset, well represented by both 614 variants, not all approaches showed conclusive signal selection. Population genetic analysis indicates that 614G increases relative 614D manner...
Several major invasive bacterial pathogens are encapsulated. Expression of a polysaccharide capsule is essential for survival in the blood, and thus virulence, but also target host antibodies basis effective vaccines. Encapsulated species typically exhibit antigenic variation express one number immunochemically distinct capsular polysaccharides that define serotypes. We provide sequences biosynthetic genes all 90 serotypes Streptococcus pneumoniae relate these to known structures patterns...
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...
Phylogeographical analyses have become commonplace for a myriad of organisms with the advent cheap DNA sequencing technologies. Bayesian model-based clustering is powerful tool detecting important patterns in such data and can be used to decipher even quite subtle signals systematic differences molecular variation. Here, we introduce two upgrades Analysis Population Structure (BAPS) software, which enable 1) spatially explicit modeling variation sequences 2) hierarchical sequence reveal...
Abstract Summary Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesizing and integrating different types analysis across millions base pairs hundreds or thousands isolates. Current approaches often use static representations phylogenetic, epidemiological, statistical evolutionary results that are difficult to relate one another. Phandango is an interactive application running a web browser allowing fast exploration large-scale combining...
The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. is suspected that associated with more severe disease than previously dominant alpha (B.1.1.7) variant. We aimed characterise severity of compared by determining relative risk hospital attendance outcomes.
Panzootic chytrid fungus out of Asia Species in the fungal genus Batrachochytrium are responsible for severe declines populations amphibians globally. The sources these pathogens have been uncertain. O'Hanlon et al. used genomics on a panel more than 200 isolates to trace source frog pathogen B. dendrobatidis hyperdiverse hotspot Korean peninsula (see Perspective by Lips). Over past century, trade amphibian species has accelerated, and now all lineages occur traded amphibians; become...
Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause hospital community-acquired infection. We aimed to map geographic distribution dominant clones that invasive infections in Europe.In each country, staphylococcal reference laboratories secured participation sufficient number achieve national geo-demographic representation. Participating collected successive methicillin-susceptible (MSSA) MRSA isolates from patients...
ABSTRACT A collection of 147 isolates Burkholderia pseudomallei , B. mallei and thailandensis was characterized by multilocus sequence typing (MLST). The 128 the causative agent melioidosis, were obtained from diverse geographic locations, humans animals with disease, environment resolved into 71 types. utility MLST scheme for epidemiological investigations established analyzing captive marine mammals birds in Hong Kong melioidosis. gave a level resolution similar to that given pulsed-field...
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...
We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase affinity the ACE2 confer antibody escape. In vitro, we show that, although itself is not an evasion mechanism, it increases infectivity associated with enhanced incorporation cleaved into virions. able partially rescue proteins that have acquired Y453F escape...
Lineage dynamics The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. United Kingdom has contributed more than 26,000 sequences to this effort. This volume data allowed du Plessis et al. develop a detailed picture the influxes virus reaching U.K. shores as pandemic developed during first months 2020 (see Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international 1000 lineages become...
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,...
In large metropolitan areas, which typically have the highest rates of gonorrhea, identification chains transmission by use partner notification is problematic, and there an increasing interest in applying molecular approaches, would require new discriminatory high-throughput procedures for recognizing clusters indistinguishable gonococci, that identify local transmission. Sequencing internal fragments 2 highly polymorphic loci, from 436 isolates recovered London during a 3-month period,...
The rapid worldwide emergence of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) is having a profound negative impact on biodiversity. However, global research efforts are fragmented and an overarching synthesis infection data lacking. Here, we provide results from community tool for compilation Bd presence report analyses collated over four-year period. Using this online database, analysed: 1) spatial taxonomic patterns infection, including families that appear over-...
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,...
Invasive pneumococcal disease remains an important health priority owing to increasing incidence caused by pneumococci expressing non-vaccine serotypes. We previously defined 621 Global Pneumococcal Sequence Clusters (GPSCs) analysing 20 027 isolates collected worldwide and from published genomic data. In this study, we aimed investigate the lineages behind predominant serotypes, mechanism of serotype replacement in disease, as well major contributing invasive post-vaccine era their...
Understanding the causes and consequences of emergence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concern is crucial to pandemic control yet difficult achieve because they arise in context variable human behavior immunity. We investigated spatial invasion dynamics lineage B.1.1.7 by jointly analyzing UK mobility, virus genomes, community-based polymerase chain reaction data. identified a multistage process which early growth rates were associated with mobility...