A5012593448- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Escherichia coli research studies
- Antibiotic Resistance in Bacteria
- Viral gastroenteritis research and epidemiology
- Viral Infections and Outbreaks Research
- Salmonella and Campylobacter epidemiology
- Vibrio bacteria research studies
- Bacterial Identification and Susceptibility Testing
- Pneumonia and Respiratory Infections
- COVID-19 epidemiological studies
- Mycobacterium research and diagnosis
- Clostridium difficile and Clostridium perfringens research
- Bacterial Infections and Vaccines
- SARS-CoV-2 and COVID-19 Research
- RNA and protein synthesis mechanisms
- Streptococcal Infections and Treatments
- Viral Infections and Vectors
- Legume Nitrogen Fixing Symbiosis
- Cancer survivorship and care
- Mindfulness and Compassion Interventions
- Disaster Response and Management
- Evolution and Genetic Dynamics
- Microbial infections and disease research
- Neonatal and Maternal Infections
University of Bath
2018-2024
Public Health England
2014-2019
European Molecular Biology Laboratory
2017-2019
Center for Disease Dynamics, Economics & Policy
2018
Boston University
2018
Harvard University
2018
University of Edinburgh
2017
Bernhard Nocht Institute for Tropical Medicine
2016
Barts Health NHS Trust
2016
National Health Service
2016
National surveillance of gastrointestinal pathogens, such as Shiga toxin-producing Escherichia coli O157 (STEC O157), is key to rapidly identifying linked cases in the distributed food network facilitate public health interventions. In this study, we used whole-genome sequencing (WGS) a tool inform national STEC terms and clusters guiding epidemiological investigation.We retrospectively analyzed 334 isolates randomly sampled from 1002 strains received by Gastrointestinal Bacteria Reference...
Abstract Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment and outcomes. Here, we present method called ‘genomic neighbour typing’ inferring the phenotype bacterial sample by identifying its closest relatives in database genomes with metadata. We show this technique can infer susceptibility...
Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with (MSM). Multidrug resistance in S. common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant was reported the United Kingdom. Here, we aimed to identify genetic basis, evolutionary history, international...
In England in 2015, Shigella sonnei isolates from men who have sex with produced extended-spectrum β-lactamases and exhibited macrolide resistance. Whole-genome sequencing showed a close relationship among the isolates, which harbored plasmid that was previously identified shigellosis outbreak this population but has acquired mobile element.
Following a large outbreak of foodborne gastrointestinal (GI) disease, multiplex PCR approach was used retrospectively to investigate faecal specimens from 88 the 413 reported cases. Gene targets range bacterial GI pathogens were detected, including Salmonella species, Shigella species and Shiga toxin-producing Escherichia coli, with majority (75%) being positive for aggR associated Enteroaggregative E. coli (EAEC) group. The 20 isolates EAEC recovered exhibited serotypes, most frequent...
Human Ebola infection is characterized by a paralysis of the immune system. A signature αβ T cells in fatal has been recently proposed, while involvement innate protection/pathogenesis unknown. Aim this study was to analyze γδ and NK patients from outbreak 2014-2015 occurred West Africa, assess their association with clinical outcome.Nineteen Ebola-infected were enrolled at time admission Treatment Centre Guinea. Patients divided two groups on basis outcome. The analysis performed using...
Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae is thought to be important adaptation and evolution of this pathogen. While competent pneumococci are able scavenge DNA added laboratory cultures, large-scale transfers multiple kb rare under these conditions. We used whole genome sequencing (WGS) map recombinants arising from contact cells with non-competent 'target' cells, using strains known genomes, distinguished by a total ~16,000 SNPs....
Abstract Background In 2015, the laboratory at Ebola treatment center in Coyah, Guinea, confirmed virus disease (EVD) 286 patients. The cycle threshold (Ct) of an virus–specific reverse transcription–polymerase chain reaction assay and 13 blood chemistry parameters were measured on admission during hospitalization. Favipiravir was offered to patients with EVD a compassionate-use basis. Methods To reduce biases raw field data, we carefully selected 163 for retrospective study assess...
Salmonella enterica serovar Enteritidis is one of the most frequent causes Salmonellosis globally and commonly transmitted from animals to humans by consumption contaminated foodstuffs. In UK many other countries in Global North, a significant proportion cases are caused imported food products or contracted during foreign travel, therefore, making rapid identification geographical source new infections requirement for robust public health outbreak investigations. Herein, we detail...
Enterohaemorrhagic Escherichia coli (EHEC) O157 is a zoonotic pathogen for which colonization of cattle and virulence in humans associated with multiple horizontally acquired genes, the majority present active or cryptic prophages. Our understanding evolution phylogeny EHEC continues to develop primarily based on core genome analyses; however, such short-read sequences have limited value analysis prophage content its chromosomal location. In this study, we applied Single Molecule Real Time...
Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided outbreak strains into sub-clusters separated by only three single-nucleotide polymorphisms in core while traditional typing identified them as separate phage types, PT8 PT54. Isolates did not cluster with local but...
ABSTRACT Experiments using bacteriophage (phage) to infect bacterial strains have helped define some basic genetic concepts in microbiology, but our understanding of the complexity bacterium-phage interactions is still limited. As global threat antibiotic resistance continues increase, phage therapy has reemerged as an attractive alternative or supplement treating antibiotic-resistant infections. Further, long-used method typing classify being replaced by molecular techniques. Thus, there a...
Abstract Background Young adults affected by cancer face physical and psychological challenges desire online supportive care. Yoga can be delivered may improve outcomes. Yet, yoga has rarely been studied with young cancer. To address this, an 8-week intervention was developed, a pilot study deemed necessary to explore feasibility, acceptability, implementation, potential benefits. Methods A mixed-methods, single-arm hybrid effectiveness-implementation evaluating the conducted. Feasibility...
Shiga toxin producing Escherichia coli O157 can cause severe bloody diarrhea and haemolytic uraemic syndrome. Phage typing of E. facilitates public health surveillance outbreak investigations, certain phage types are more likely to occupy specific niches associated with age groups disease severity. The aim this study was analyse the genome sequences 16 (fourteen T4 two T7) phages determine genes responsible for subtle differences in type profiles. were sequenced using paired-end Illumina...
Genomics, combined with population mobility data, used to map importation and spatial spread of SARS-CoV-2 in high-income countries has enabled the implementation local control measures. Here, track lineages Bangladesh at national level, we analysed outbreak trajectory variant emergence using genomics, Facebook 'Data for Good' data from three mobile phone operators. We sequenced complete genomes 67 samples (collected by IEDCR between March July 2020) these 324 publicly available Global...
Whole genome sequencing in conjunction with traditional epidemiology has been used to reconstruct transmission networks of Mycobacterium tuberculosis during outbreaks. Given its low mutation rate, genetic diversity within M. outbreaks can be extremely limited – making it difficult determine precisely who transmitted whom. In addition consensus SNPs (cSNPs), examining heterogeneous alleles (hSNPs) proposed improve resolution. However, few studies have examined the potential biases detecting...
Temperate bacteriophages are a common feature of Pseudomonas aeruginosa genomes, but their role in chronic lung infections is poorly understood. This study was designed to identify the diverse communities mobile P. phages by employing novel metagenomic methods, determine cross infectivity, and demonstrate influence phage infection on antimicrobial susceptibility. Mixed temperate populations were chemically mobilized from individual aeruginosa, isolated patients with cystic fibrosis (CF) or...
Shigellosis in men who have sex with (MSM) is caused by multidrug resistant Shigellae, exhibiting resistance to antimicrobials including azithromycin, ciprofloxacin and more recently the third-generation cephalosporins. We sequenced four blaCTX-M-27-positive MSM Shigella isolates (2018-20) using Oxford Nanopore Technologies; three S. sonnei (identified as two clade 2, one 5) flexneri 3a, explore AMR context. All harboured Tn7/Int2 chromosomal integrons, whereas 3a contained Resistance Locus....
Abstract Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empiric antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could impact patient treatment and outcomes. Here we present method called ‘genomic neighbor typing’ inferring the phenotype bacterial sample by identifying its closest relatives in database genomes with metadata. We show this technique can infer susceptibility...
Understanding how antimicrobial resistance spreads is critical for optimal application of new treatments. In the naturally competent human pathogen Streptococcus pneumoniae , to β-lactam antibiotics mediated by recombination events in genes encoding target proteins, resulting reduced drug binding affinity. However, front-line antibiotic amoxicillin, exact mechanism still needs be elucidated. Through successive rounds transformation with genomic DNA from a clinically resistant isolate, we...
Abstract Background Klebsiella pneumoniae (Kp) is an important pathogen of humans and animals, recent reports ‘convergent’ strains that carry both virulence antimicrobial resistance genes (ARGs) have raised serious public health concern. The plasmid-borne iuc locus, encoding the siderophore aerobactin, a key factor in this species. variant 3 associated with porcine human clinical isolates carried by mostly uncharacterised IncF plasmids. Methods We used combination short-read long-read...
The ENGAGE project (http://www.engage-europe.eu/) was a collaboration between eight institutions across Europe. aim to boost the scientific cooperation use whole genome sequencing (WGS) analysis in food safety and public health protection. focused on Escherichia coli (commensal E. coli) different Salmonella spp. serotypes. A total of 3,360 genomes, 778 2,582 Salmonella, respectively, were produced. These genomes stored shared among partners temporary repository be submitted European...