A5026480684- Antibiotic Resistance in Bacteria
- Mycobacterium research and diagnosis
- SARS-CoV-2 and COVID-19 Research
- Bacterial Identification and Susceptibility Testing
- Tuberculosis Research and Epidemiology
- Clostridium difficile and Clostridium perfringens research
- Antimicrobial Resistance in Staphylococcus
- SARS-CoV-2 detection and testing
- Genomics and Phylogenetic Studies
- COVID-19 Clinical Research Studies
- Antibiotic Use and Resistance
- Pneumonia and Respiratory Infections
- Respiratory viral infections research
- Gut microbiota and health
- Viral gastroenteritis research and epidemiology
- Malaria Research and Control
- Microscopic Colitis
- COVID-19 epidemiological studies
- Hemoglobinopathies and Related Disorders
- Iron Metabolism and Disorders
- Antibiotics Pharmacokinetics and Efficacy
- Streptococcal Infections and Treatments
- Bacterial Infections and Vaccines
- Infective Endocarditis Diagnosis and Management
- HIV Research and Treatment
University of Oxford
2016-2025
National Institute for Health Research
2016-2025
Oxford University Hospitals NHS Trust
2015-2024
John Radcliffe Hospital
2015-2024
Oxford BioMedica (United Kingdom)
2015-2024
Imperial College London
2022-2024
University College London
1997-2024
The Royal Free Hospital
2024
Anthony Nolan
2024
Oxford Biomedical Research
2013-2023
BackgroundThe relationship between the presence of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and risk subsequent reinfection remains unclear.MethodsWe investigated incidence SARS-CoV-2 infection confirmed by polymerase chain reaction (PCR) in seropositive seronegative health care workers attending testing asymptomatic symptomatic staff at Oxford University Hospitals United Kingdom. Baseline antibody status was determined anti-spike (primary analysis)...
BackgroundTuberculosis incidence in the UK has risen past decade. Disease control depends on epidemiological data, which can be difficult to obtain. Whole-genome sequencing detect microevolution within Mycobacterium tuberculosis strains. We aimed estimate genetic diversity of related M strains Midlands and investigate how this measurement might used community outbreaks.MethodsIn a retrospective observational study, we Illumina technology sequence genomes from an archive frozen cultures....
Intrapleural fibrinolytic agents are used in the drainage of infected pleural-fluid collections. This use is based on small trials that did not have statistical power to evaluate accurately important clinical outcomes, including safety. We conducted a trial clarify therapeutic role intrapleural streptokinase.In this double-blind trial, 454 patients with pleural infection (defined by presence purulent fluid or pH below 7.2 signs proven bacterial invasion space) were randomly assigned receive...
ABSTRACT A prospective study was performed to establish criteria for the microbiological diagnosis of prosthetic joint infection at elective revision arthroplasty. Patients were treated in a multidisciplinary unit dedicated management and musculoskeletal infection. Standard multiple samples periprosthetic tissue obtained surgery, Gram stained, cultured by direct enrichment methods. With reference histology as criterion standard, sensitivities, specificities, likelihood ratios (LRs)...
By use of multilocus sequence typing, Streptococcus pneumoniae isolates causing invasive disease (n=150) were compared with those from nasopharyngeal carriage (n=351) among children in Oxford. The prevalence individual clones (sequence types) and serotypes was related to their carriage, an odds ratio (OR) for calculated the major serotypes. All carried caused disease, although ability do so varied greatly. Thus, 2 serotype 14 ∼10-fold overrepresented isolates, whereas a 3 clone...
It has been thought that Clostridium difficile infection is transmitted predominantly within health care settings. However, endemic spread hampered identification of precise sources and the assessment efficacy interventions.
Abstract The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection drug resistance in clinical samples, and improvements global surveillance. Here we show how de Bruijn graph representation bacterial diversity can be used identify species profiles isolates. We implement this method Staphylococcus aureus Mycobacterium tuberculosis a software package (‘Mykrobe predictor’) that takes raw sequence data as input, generates clinician-friendly report within 3 minutes...
The effectiveness of the BNT162b2 and ChAdOx1 vaccines against new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections requires continuous re-evaluation, given increasingly dominant B.1.617.2 (Delta) variant. In this study, we investigated these in a large, community-based survey randomly selected households across United Kingdom. We found that (new polymerase chain reaction (PCR)-positive cases) with symptoms or high viral burden is reduced variant (absolute difference...
Before the emergence of B.1.617.2 (delta) variant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), vaccination reduced transmission SARS-CoV-2 from vaccinated persons who became infected, potentially by reducing viral loads. Although still lowers risk infection, similar loads in and unvaccinated are infected with delta call into question degree to which prevents transmission.We used contact-testing data England perform a retrospective observational cohort study involving adult...
A robust high-throughput multilocus sequence typing (MLST) scheme for Clostridium difficile was developed and validated using a diverse collection of 50 reference isolates representing 45 different PCR ribotypes 102 from recent clinical samples. total 49 were represented overall. All typed by MLST yielded 40 types (STs). web-accessible database set up (http://pubmlst.org/cdifficile/) to facilitate the dissemination comparison C. genotyping data among laboratories. ribotyping similar in...
Artemisinin (qinghaosu) and its derivatives are rapidly effective antimalarial drugs derived from a Chinese plant. Preliminary studies suggest that these may be more than quinine in the treatment of severe malaria. We studied artemether Vietnam, where Plasmodium falciparum has reduced sensitivity to quinine.
Candida auris is an emerging and multidrug-resistant pathogen. Here we report the epidemiology of a hospital outbreak C. colonization infection.After identification cluster infections in neurosciences intensive care unit (ICU) Oxford University Hospitals, United Kingdom, instituted patient environmental screening program package interventions. Multivariable logistic regression was used to identify predictors infection. Isolates from patients environment were analyzed by whole-genome...
<h2>Summary</h2><h3>Background</h3> Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic in 2020. Testing is crucial for mitigating public health and economic effects. Serology considered key to population-level surveillance potentially individual-level risk assessment. However, immunoassay performance not been compared on large, identical sample sets. We aimed investigate the of four high-throughput commercial SARS-CoV-2 antibody immunoassays novel...
Nature Communications 6: Article number: 10063 (2015); Published: 21 December 2015; Updated: 20 April 2016 In Supplementary Data 3 of this Article, one the Staphylococcus aureus accession codes is incorrect, as follows: SRR2101499 should be ERR1197981.
Patterns and bottlenecks A year into the severe acute respiratory syndrome coronavirus 2 pandemic, we are experiencing waves of new variants emerging. Some these have worrying functional implications, such as increased transmissibility or antibody treatment escape. Lythgoe et al. undertaken in-depth sequencing more than 1000 hospital patients' isolates to find out how virus is mutating within individuals. Overall, there seem be consistent reproducible patterns within-host diversity. The...
ABSTRACT Routine full characterization of Mycobacterium tuberculosis is culture based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain information for global surveillance; such data could be transformative if provided at or near the point care. We demonstrate a low-cost method DNA extraction directly from patient samples M. WGS. initially evaluated by using Illumina MiSeq sequencer (40 smear-positive...
Whole-genome sequencing (WGS) could potentially provide a single platform for extracting all the information required to predict an organism's phenotype. However, its ability accurate predictions has not yet been demonstrated in large independent studies of specific organisms. In this study, we aimed develop genotypic prediction method antimicrobial susceptibilities. The whole genomes 501 unrelated Staphylococcus aureus isolates were sequenced, and assembled interrogated using BLASTn panel...
The effectiveness of COVID-19 vaccination in preventing new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections the general community is still unclear. Here, we used Office for National Statistics Infection Survey-a large community-based survey individuals living randomly selected private households across United Kingdom-to assess BNT162b2 (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca; ChAdOx1) vaccines against any SARS-CoV-2 PCR-positive tests, split...
Whole-genome sequencing potentially represents a single, rapid and cost-effective approach to defining resistance mechanisms predicting phenotype, strain type, for both clinical epidemiological purposes. This retrospective study aimed determine the efficacy of whole genome-based antimicrobial prediction in isolates Escherichia coli Klebsiella pneumoniae. Seventy-four E. 69 K. pneumoniae bacteraemia from Oxfordshire, UK, were sequenced (Illumina HiSeq 2000). Resistance phenotypes predicted...