A5064392122- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- COVID-19 epidemiological studies
- Viral gastroenteritis research and epidemiology
- Bacteriophages and microbial interactions
- Gut microbiota and health
- vaccines and immunoinformatics approaches
- Legume Nitrogen Fixing Symbiosis
- Salmonella and Campylobacter epidemiology
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Escherichia coli research studies
- Immune responses and vaccinations
- Plant Virus Research Studies
- Urinary Tract Infections Management
- Plant-Microbe Interactions and Immunity
- Barrier Structure and Function Studies
- Insect symbiosis and bacterial influences
- Inflammasome and immune disorders
- Behavioral and Psychological Studies
- Entomopathogenic Microorganisms in Pest Control
- Monoclonal and Polyclonal Antibodies Research
- Bacterial Infections and Vaccines
Quadram Institute
2020-2024
Norwich Research Park
2012-2024
University of East Anglia
2023
Imperial College London
2022
University of Cambridge
2021
University College London
2021
Isomerase Therapeutics (United Kingdom)
2017
Teagasc - The Irish Agriculture and Food Development Authority
2014
University College Dublin
2014
John Innes Centre
2012
Altered intestinal microbiota composition in later life is associated with inflammaging, declining tissue function, and increased susceptibility to age-associated chronic diseases, including neurodegenerative dementias. Here, we tested the hypothesis that manipulating influences development of major comorbidities aging and, particular, inflammation affecting brain retina.
We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > Illumina NextSeq) depending changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by 2 plates containing 95 59 nanopore platforms comparing to LoCost method. Of 154 samples sequenced using all 3 methods, ≥ 90% genome coverage obtained 64.3% LoCost, 71.4%...
Abstract Erythromycin, avermectin and rapamycin are clinically useful polyketide natural products produced on modular synthase multienzymes by an assembly-line process in which each module of enzymes turn specifies attachment a particular chemical unit. Although encoding genes have been successfully engineered to produce novel analogues, the can be relatively slow, inefficient, frequently low-yielding. We now describe method for rapidly recombining gene clusters replace, add or remove...
The COVID-19 pandemic has spread rapidly throughout the world. In UK, initial peak was in April 2020; county of Norfolk (UK) and surrounding areas, which a stable, low-density population, over 3200 cases were reported between March August 2020. As part activities national Genomics Consortium (COG-UK) we undertook whole genome sequencing SARS-CoV-2 genomes present positive clinical samples from region. These collected by four major hospitals, multiple minor care facilities community...
Salmonella is a significant public health pathogen responsible for wide spectrum of diseases, ranging from gastroenteritis to invasive non-typhoidal salmonellosis (iNTS) and enteric fever. Although advancements in whole genome sequencing (WGS) have improved surveillance outbreak investigations, traditional single-colony methods overlook within-host diversity, potentially underestimating the complexity infections. This study explores genome-wide diversity strains recovered stool samples eight...
The gastrointestinal tract harbors the gut microbiota, structural alterations of which (dysbiosis) are linked with an increase in permeability ("leaky gut"), enabling luminal antigens and bacterial products such as nanosized extracellular vesicles (BEVs) to access circulatory system. Blood-derived BEVs contain various cargoes may be useful biomarkers for diagnosis monitoring disease status relapse conditions inflammatory bowel (IBD). To progress this concept, we developed a rapid,...
Abstract Background Urinary tract infections (UTIs) are a frequent cause for visits to primary care providers. In alignment globally, uropathogenic Escherichia coli (UPEC) the main aetiological agent UTIs in Norfolk and increasingly difficult treat due multi-drug resistance. Objectives We set out identify which clonal groups resistance genes disseminating community hospitals Norfolk, first study of its kind UPEC this region. Methods collected 199 clinical E. isolates causing hospital from...
Two expression vectors utilizing the inducible taurine promoter (tauAp) were developed. Plasmid pLMB51 is a stable low-copy vector enabling in environment and planta. The higher copy number pLMB509 enables BD restriction-independent cloning, expression, purification of polyhistidine-tagged proteins.
Abstract Background Recently it has been shown that Ensifer adhaerens can be used as a plant transformation technology, transferring genes into several genomes when equipped with Ti plasmid. For this study, we have sequenced the genome of OV14 (OV14) and compared those Agrobacterium tumefaciens C58 (C58) Sinorhizobium meliloti 1021 (1021); latter which also demonstrated capacity to genetically transform crop genomes, albeit at significantly reduced frequencies. Results The 7.7 Mb comprises...
Four bacterial strains were isolated from two different colony sources of the wax moth Galleria mellonella. They characterized by a polyphasic approach including 16S rRNA gene sequence analysis, core-genome average nucleotide identity (ANI) digital DNA-DNA hybridization (dDDH), determination G+C content, screening antibiotic resistance genes, and various phenotypic analyses. Initial analysis identities indicated that strain GAL7T was potentially very closely related to Enterococcus...
Abstract The COVID-19 pandemic has spread rapidly throughout the world. In UK, initial peak was in April 2020; county of Norfolk (UK) and surrounding areas, which a stable, low-density population, over 3,200 cases were reported between March August 2020. As part activities national Genomics Consortium (COG-UK) we undertook whole genome sequencing SARS-CoV-2 genomes present positive clinical samples from region. These collected by four major hospitals, multiple minor care facilities community...
Abstract The COVID-19 pandemic has spread to almost every country in the world since it started China late 2019. Controlling requires a multifaceted approach including whole genome sequencing support public health interventions at local and national levels. One of most widely used methods for is ARTIC protocol, tiling PCR followed by Oxford Nanopore (ONT) up 96 samples time. There need, however, flexible, platform agnostic, method that can provide multiple throughput options depending on...
Background Förster resonance energy transfer (FRET) biosensors are powerful tools to detect biologically important ligands in real time. Currently FRET bisosensors available for twenty-two compounds distributed eight classes of chemicals (two pentoses, two hexoses, disaccharides, four amino acids, one nucleobase, nucleotides, six ions and three phytoestrogens). To expand the number we used induction profile Sinorhizobium meliloti transportome systematically screen new biosensors....
Abstract Background Campylobacter jejuni and coli are the major causative agents of bacterial gastroenteritis worldwide known obligate microaerophiles. Despite being sensitive to oxygen its reduction products, both species readily isolated from animal food products kept under atmospheric conditions where they face high tension levels. Results In this study, Transposon Directed Insertion-site Sequencing (TraDIS) was used investigate ability one C. strain two strains overcome oxidative stress,...
Abstract Background Campylobacter jejuni is a pervasive pathogen of major public health concern with complex ecology requiring accurate and informative approaches to define diversity during outbreak investigations. Source attribution analysis may be confounded if the genetic C. population not adequately captured in single specimen. The aim this study was determine genomic within individual stool specimens from four campylobacteriosis patients. Direct plating pre-culture filtration one...
The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including Indian sub-continent. Pakistan has one world's largest populations, over 200 million people and is experiencing a severe third wave infections caused by that began March 2021. In Pakistan, during until now only 12 genomes have been collected among these nine are from Islamabad. This highlights need for more genome sequencing allow surveillance variants circulation. fact,...
Abstract Background The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including Indian sub-continent. Pakistan has one world ‘s largest population, over 200 million people and is experiencing a severe third wave infections caused by that begun March 2021.In Pakistan, during until now only 12 genomes have been collected among these 9 are from Islamabad. This highlights need for more genome sequencing allow surveillance variants...
Abstract Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where repeat units are longer than read length. To overcome this limitation, we have developed using Oxford Nanopore technology that generates and uses long reads; called LoRTIS (Long-Read...
Altered intestinal microbiota composition in later life is associated with inflammaging and increased susceptibility to age–associated chronic diseases affecting various organs. Here we tested the hypothesis that manipulating influences development of comorbidities aging, particular, inflammation epithelial barrier integrity, retina, brain. Using heterochronic transplantation exchange young (3 month), old (18 aged (24 month) mice, show increases permeability, central nervous system (CNS)...
Synopsis Background Half of all women have experienced a urinary tract infection (UTI) in their lifetime and this remains persistent issue rural counties like Norfolk, UK. In alignment globally, Uropathogenic E. coli (UPEC) are the main etiological agent for UTIs Norfolk increasingly difficult to treat due multi-drug resistance (MDR). Objective We set out identify which clonal groups genes disseminating community hospitals first study its kind UPEC region. Methods collected 217 clinical...