A5021655313- Antibiotic Resistance in Bacteria
- Salmonella and Campylobacter epidemiology
- Bacteriophages and microbial interactions
- Pharmaceutical and Antibiotic Environmental Impacts
- Genomics and Phylogenetic Studies
- Bacterial Identification and Susceptibility Testing
- Viral gastroenteritis research and epidemiology
- Veterinary medicine and infectious diseases
- Escherichia coli research studies
- Enterobacteriaceae and Cronobacter Research
- Molecular Biology Techniques and Applications
- Gut microbiota and health
- Mycobacterium research and diagnosis
- Microbial infections and disease research
- Antimicrobial Resistance in Staphylococcus
- Bacterial biofilms and quorum sensing
- Cancer Genomics and Diagnostics
- Bacterial Genetics and Biotechnology
- Plant Pathogenic Bacteria Studies
- Antibiotics Pharmacokinetics and Efficacy
- Aquaculture disease management and microbiota
- Vibrio bacteria research studies
- Pneumonia and Respiratory Infections
- Microbial Metabolic Engineering and Bioproduction
- Animal Nutrition and Physiology
Animal and Plant Health Agency
2015-2024
Public Health England
2020-2021
National Institute for Health Research
2017-2021
University of Oxford
2017-2021
Veterinary Medicines Directorate
2005-2018
Ain Shams University
2017
To determine the occurrence of mcr-1 and mcr-2 genes in Gram-negative bacteria isolated from healthy pigs Great Britain. (n = 657) between 2014 2015 were examined by WGS. Variants identified Moraxella spp. pooled caecal contents at slaughter collected six farms Other bacteria, including Escherichia coli same farms, not detected harbouring or mcr-2. A porci-like isolate, MSG13-C03, harboured MCR-1.10 with 98.7% identity to MCR-1, we describe first detection mcr-6.1, found on chromosome...
Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete assembly. Long-read greatly assists with resolving complex genomes, particularly when combined short-read data (hybrid assembly). However, it is clear how different long-read methods affect hybrid assembly accuracy. Relative automation of the process also crucial to facilitating high-throughput reconstruction, avoiding multiple bespoke filtering...
Microevolution associated with emergence and expansion of new epidemic clones bacterial pathogens holds the key to epidemiologic success. To determine microevolution monophasic Salmonella Typhimurium during an epidemic, we performed comparative whole-genome sequencing phylogenomic analysis isolates from United Kingdom Italy 2005-2012. These formed a single clade distinct recent previously described North America Spain. The UK showed novel genomic island encoding resistance heavy metals...
The objective of this study was to characterize colistin-resistant bacteria isolated from pigs on a farm in Great Britain following identification plasmid-borne colistin resistance mechanism Escherichia coli China.Phenotypic antimicrobial susceptibility testing undertaken by broth dilution and WGS performed detect the presence genes encoding virulence. Transferable investigated conjugation.Two E. one Salmonella Typhimurium variant Copenhagen were shown be MDR, including colistin, with...
Abstract Background Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many approaches inferring taxonomic composition AMR gene content complex community samples from shotgun metagenomic data, but there has been little work establishing optimum sequencing depth, data processing analysis methods these samples. In this study we cultured...
The pangenome of Escherichia coli from nearby farms shows how livestock host and local geography shape bacterial populations.
ABSTRACT Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete assembly. Long read greatly assists with resolving complex genomes, particularly when combined short-read data (hybrid assembly). However, it is clear how different long-read methods impact on assembly accuracy. Relative automation of the process also crucial to facilitating high-throughput reconstruction, avoiding multiple bespoke...
Combatting antimicrobial resistant (AMR) using a One-Health approach is essential as various bacteria, including Escherichia coli , common are becoming increasingly and livestock may be reservoir. The AMR gene content of 492 E. isolated from 56 pig farms across Great Britain in 2014–2015, purified on antibiotic selective non-selective plates, was determined whole genome sequencing (WGS). were phylogenetically diverse harboring variety profiles with widespread resistance to “old” antibiotics;...
Salmonella spp. is a leading cause of gastrointestinal enteritis in humans where it largely contracted via contaminated poultry and pork. Phages can be used to control infection the animals, which could break cycle before products are accessible for consumption. Here, potential 21 myoviruses siphovirus eliminate vitro vivo was examined with aim developing biocontrol strategy curtail swine. Together, phages targeted twenty-three ten swine prevalent serotype isolates tested. Although...
The cytolethal distending toxin (CDT) of Campylobacter jejuni was detectable, using an in vitro assay, most but not all 24 strains tested. reason for the absence activity these naturally occurring CDT-negative C. then investigated at genetic level. CDT is encoded by three highly conserved genes, cdtA, -B, and -C. In strains, two types mutation were identified. activities possessing both successfully complemented with functional genes 11168. first type comprised a 667-bp deletion across cdtA...
Salmonella are closely related to commensal Escherichia coli but have gained virulence factors enabling them behave as enteric pathogens. Less well studied the similarities and differences that exist between metabolic properties of these organisms may contribute toward niche adaptation To address this, we constructed a genome scale model (iMA945). The comprises 945 open reading frames or genes, 1964 reactions, 1036 metabolites. There was significant overlap with genes present in E. MG1655...
Campylobacter jejuni is a major cause of human inflammatory enteritis, but colonizes the gastrointestinal tract poultry to high level in commensal manner. In vitro, C. induces production cytokines from both and avian-model epithelial cell macrophage infections. This suggests that, vivo, could induce proinflammatory signals hosts. We investigated whether cytokine response can be measured day-of-hatch 2-week-old Light Sussex chickens during infection with jejuni. A significant induction...
In recent years, there has been an increase in the number of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 recovered from S. isolated animals UK. To determine possible origins 12 LA-MRSA CC398 isolates collected after screening more than a thousand animal UK between 2013 and 2015, whole genome sequences (WGS) European, including UK, non-European diverse hosts were compared. Phylogenetic reconstruction applied to WGS data assess genetic...
Background Surveillance of commensal Escherichia coli , a possible reservoir antimicrobial resistance (AMR) genes, is important as they pose risk to human and animal health. Most surveillance activities rely on phenotypic characterisation, but whole genome sequencing (WGS) presents an alternative. Aim In this retrospective study, we tested 515 E. isolated from pigs evaluate the use WGS predict phenotype. Methods Minimum inhibitory concentration (MIC) was determined for nine antimicrobials...
Resistance to amoxicillin-clavulanate, a widely used beta-lactam/beta-lactamase inhibitor combination antibiotic, is rising globally, and yet susceptibility testing remains challenging. To test whether whole-genome sequencing (WGS) could provide more reliable assessment of than traditional methods, we predicted resistance from WGS for 976 Escherichia coli bloodstream infection isolates Oxfordshire, United Kingdom, comparing against phenotypes the BD Phoenix (calibrated EUCAST guidelines).
Enterobacterales from livestock are potentially important reservoirs for antimicrobial resistance (AMR) to pass through the food chain humans, thereby increasing AMR burden and affecting our ability tackle infections. In this study 168 isolates four genera of order , primarily Escherichia coli were purified (cattle, pigs sheep) faeces 14 farms in United Kingdom. Their genomes resolved using long- short-read sequencing analyse genes their genetic context, as well explore relationship between...
Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, extent plasmid sharing and evolution between causing human infections other niches remains unclear, including emergence plasmids. Dense, unselected sampling is essential to developing our understanding epidemiology designing appropriate interventions limit plasmid-associated AMR. We established geographically temporally restricted...
There are concerns that antimicrobial usage (AMU) is driving an increase in multi-drug resistant (MDR) bacteria so treatment of microbial infections becoming harder humans and animals. The aim this study was to evaluate factors, including usage, affect resistance (AMR) on farm over time.A population 14 cattle, sheep pig farms within a defined area England were sampled three times year collect data AMR faecal Enterobacterales flora; AMU; husbandry or management practices. Ten pooled samples...
Antimicrobial resistance (AMR) is a global health hazard. Although clinical and agricultural environments are well-established contributors to the evolution dissemination of AMR, research on wastewater treatment works (WwTWs) has highlighted their potential role as disseminators AMR in freshwater environments. Using metagenomic sequencing analysis, we investigated changes resistomes associated mobile genetic elements within untreated influents treated effluents five WwTWs, sediments...
The anaerobic spirochaete Brachyspira pilosicoli causes enteric disease in avian, porcine and human hosts, amongst others. To date, the only available genome sequence of B. is that strain 95/1000, a isolate. In first intra-species comparison within genus, we report whole B2904, an avian isolate, incomplete WesB, comparisons with 95/1000. We also draw on sequences from three other species. Finally application high-throughput Biolog phenotype screening tool strains for detailed between...
The opportunistic human pathogen, Pseudomonas aeruginosa, is a major cause of infections in chronic wounds, burns and the lungs cystic fibrosis patients. P. aeruginosa genome encodes at least three proteins exhibiting characteristic domain structure autotransporters, but much remains to be understood about functions these their role pathogenicity. Autotransporters are largest family secreted Gram-negative bacteria, those characterised virulence factors. Here, we demonstrate that PA0328...
Salmonella enterica is a zoonotic foodborne pathogen that causes acute gastroenteritis in humans. We assessed the virulence potential of one-hundred and six strains isolated from food animals products. A high through-put genes microarray demonstrated Pathogenicity Islands (SPI) adherence were highly conserved, while prophages plasmid variably present. Isolates grouped by serotype, plasmids separated S. Typhimurium two clusters. Atypical results lead to whole genome sequencing (WGS) Infantis...
Between 2011 and 2014 outbreaks of septicaemia due to Klebsiella pneumoniae subspecies (Kpp) were diagnosed on thirteen English pig farms. The most consistent features rapid deaths pigs from ten-days-old weaning, seasonal occurrence (May September), affected farms being outdoor breeding herds the location all but one in East Anglia region Eastern England. Molecular characterisation outbreak Kpp isolates showed that by multilocus sequencing sequence type 25 (ST25) K2 capsular with a...