A5071129241- Salmonella and Campylobacter epidemiology
- Viral gastroenteritis research and epidemiology
- Antimicrobial Resistance in Staphylococcus
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Bacterial biofilms and quorum sensing
- Antibiotic Resistance in Bacteria
- Escherichia coli research studies
- Aquaculture disease management and microbiota
- Probiotics and Fermented Foods
- Vibrio bacteria research studies
- Vitamin C and Antioxidants Research
- Bacterial Genetics and Biotechnology
- Bacterial Identification and Susceptibility Testing
- Microbial Metabolism and Applications
- Evolution and Genetic Dynamics
- Plant Pathogenic Bacteria Studies
- Gut microbiota and health
- Listeria monocytogenes in Food Safety
- Biomedical Text Mining and Ontologies
- Pharmaceutical and Antibiotic Environmental Impacts
- Helicobacter pylori-related gastroenterology studies
- Identification and Quantification in Food
- Cancer Research and Treatments
- RNA and protein synthesis mechanisms
University of Oxford
2022-2025
Chiang Mai University
2018-2024
Adelphi Group (United Kingdom)
2024
Ineos (United Kingdom)
2024
Ineos (Belgium)
2023
Open Data Institute
2023
University of Arizona
2023
Center for Genomic Science
2023
University of Bath
2016-2022
AO Foundation
2017-2018
The use of whole-genome phylogenetic analysis has revolutionized our understanding the evolution and spread many important bacterial pathogens due to high resolution view it provides. However, majority such analyses do not consider potential role accessory genes when inferring evolutionary trajectories. Moreover, recently discovered importance switching gene regulatory elements suggests that an exhaustive analysis, combining information from core with could provide unparalleled detail a...
Abstract Chickens are the most common birds on Earth and colibacillosis is among diseases affecting them. This major threat to animal welfare safe sustainable food production difficult combat because etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address underlying evolutionary mechanisms of extraintestinal spread systemic infection poultry. Combining...
Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding traits differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on skin and mucous membranes virtually all but a major cause nosocomial infection associated with invasive procedures. Here we address underlying evolutionary mechanisms pathogenicity combining...
Abstract Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens C ampylobacter coli and . jejuni differ from each other around 15% at the nucleotide level, corresponding an average of nearly 40 amino acids per protein‐coding gene. Using whole genome sequencing, we show that a single C. lineage, which has successfully colonized...
The opportunistic pathogens Staphylococcus aureus and epidermidis represent major causes of severe nosocomial infection, are associated with high levels mortality morbidity worldwide. These species both common commensals on the human skin in nasal pharynx, but genetically distinct, differing at 24% average nucleotide divergence 1,478 core genes. To better understand genome dynamics these ecologically similar staphylococcal species, we carried out a comparative analysis 324 S. genomes,...
Abstract Campylobacter jejuni and coli are the biggest causes of bacterial gastroenteritis in developed world, with human infections typically arising from zoonotic transmission associated infected meat. Because is not thought to survive well outside gut, host-associated populations genetically isolated varying degrees. Therefore, likely origin most strains can be determined by variation genome. This instructive for characterizing source infection. However, some common strains, notably...
The increasing availability of hundreds whole bacterial genomes provides opportunities for enhanced understanding the genes and alleles responsible clinically important phenotypes how they evolved. However, it is a significant challenge to develop easy-to-use scalable methods characterizing these large complex data relating disease epidemiology. Existing approaches typically focus on either homologous sequence variation in that are shared by all isolates, or non-homologous - focusing...
ABSTRACT Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism part commensal microbiota numerous host species, including livestock, and these animals constitute potential sources human infection. Molecular typing approaches, especially multilocus sequence (MLST), have been used to attribute source campylobacteriosis by quantifying relative abundance alleles at seven MLST loci isolates from animal reservoirs infection, implicating chicken as a...
The genomes of 262 Bacillus cereus isolates were analyzed including 69 sampled from equipment, raw milk and dairy products Brazil. population structure showed strains belonging to known phylogenetic groups II, III, IV, V VI. Almost all the obtained belonged group III. Investigation specific alleles revealed high numbers carrying toxin-associated genes cytK (53.62%), hblA (59.42%), hblC (44.93%), hblD nheA (84.06%), nheB (89.86%) nheC (84.06%) with IV having significant higher prevalence...
Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption contaminated poultry. C. lineages vary in host range and prevalence human infection, suggesting differences survival throughout poultry processing chain. From 7343 MLST-characterised isolates, we sequenced 600 coli isolates from various stages clinical cases. A genome-wide association study (GWAS) ST-21 ST-45 complexes identified genetic elements over-represented that...
Antimicrobial resistant (AMR) Campylobacter is a global health threat, however there limited information on genomic determinants of resistance in low- and middle-income countries. We evaluated AMR using collection whole genome sequenced jejuni C. coli isolates from Iquitos, Peru. two pediatric cohort studies enriched with that demonstrated to ciprofloxacin azithromycin were mined for determinants. The gyrA mutation leading the Thr86Ile amino acid change was only associated fluoroquinolone...
Summary Multicellular biofilms are an ancient bacterial adaptation that offers a protective environment for survival in hostile habitats. In microaerophilic organisms such as C ampylobacter , play key role transmission to humans the bacteria exposed atmospheric oxygen concentrations when leaving reservoir host gut. Genetic determinants of biofilm formation differ between species, but little is known about how strains same species achieve phenotype with different genetic backgrounds. Our...
The use of antimicrobials in human and veterinary medicine has coincided with a rise antimicrobial resistance (AMR) the food-borne pathogens Campylobacter jejuni coli. Faecal contamination from main reservoir hosts (livestock, especially poultry) is principal route infection but little known about spread AMR among source sink populations. In particular, questions remain how resistomes interact between species hosts, potential role sewage as conduit for AMR. Here, we investigate genomic...
Helicobacter pylori are stomach-dwelling bacteria that present in about 50% of the global population. Infection is asymptomatic most cases, but it has been associated with gastritis, gastric ulcers and cancer. Epidemiological evidence shows progression to cancer depends upon host pathogen factors, questions remain why phenotypes develop a minority infected people. Here, we use comparative genomics approaches understand how genetic variation amongst bacterial strains influences disease...
Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact microbiota, potentially increasing risk zoonotic pathogens being transmitted humans, but intensive livestock production host-associated bacteria rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked phenotype studies, understand timescale genomic adaptations associated with proliferation most common food-born...
Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to another. This has potential rapidly promote new adaptive trajectories such as zoonotic or antimicrobial resistance. However, for this occur requires gaps align barriers recombination within a given time frame. Chief among these is the physical separation of with distinct ecologies separate niches. Within genus Campylobacter, there are divergent ecologies, from rarely isolated single-host specialists...
ABSTRACT Staphylococcus epidermidis has emerged as an important opportunistic pathogen causing orthopedic-device-related infections (ODRI). This study investigated the association of genome variation and phenotypic features infecting S. isolate with clinical outcome for infected patient. isolates were collected from 104 patients ODRI. Their outcomes evaluated, after average 26 months, either “cured” or “not cured.” The tested antibiotic susceptibility biofilm formation. Whole-genome...
Fitness costs imposed on bacteria by antibiotic resistance mechanisms are believed to hamper their dissemination. The scale of these is highly variable. Some, including Staphylococcus aureus the clinically important mupirocin, have been reported as being cost-free, which suggests that there few barriers preventing global spread. However, this not supported surveillance data in healthy communities, indicate mechanism relatively unsuccessful. Epistasis analysis two collections MRSA provides an...
Bacterial plasmids can vary from small selfish genetic elements to large autonomous replicons that constitute a significant proportion of total cellular DNA. By conferring novel function the cell, may facilitate evolution but their mobility be opposed by co-evolutionary relationships with chromosomes or encouraged via infectious sharing genes encoding public goods. Here, we explore these hypotheses through large-scale examination association between and chromosomal DNA in phenotypically...
Abstract Helicobacter pylori is a common component of the human stomach microbiota, possibly dating back to speciation Homo sapiens. A history pathogen evolution in allopatry has led development genetically distinct H. subpopulations, associated with different populations, and more recent admixture among subpopulations can provide information about migrations. However, little known degree which some genes are conserved face admixture, potentially indicating host adaptation, or how virulence...
Abstract Campylobacter enterocolitis may lead to post-infection irritable bowel syndrome (PI-IBS) and while some C. jejuni strains are more likely than others cause human disease, genomic virulence characteristics promoting PI-IBS development remain uncharacterized. We combined pangenome-wide association studies phenotypic assays compare isolates from patients who developed with those did not. show that variation in bacterial stress response ( Cj0145_phoX ), adhesion protein Cj0628_CapA core...
More antibiotics are administered to livestock animals than treat human infections. Industrialization, large animal densities and early weaning mean pigs exposed more any other animal. Consequently, antimicrobial resistance (AMR) is common among commensal pathogenic bacteria. Heavy metals (HMs) also often used as feed additives for growth promotion infection prevention alongside antimicrobials, increased exposure copper, zinc cadmium can further encourage AMR through co-selection. In this...
ABSTRACT Streptomyces coelicolor contains paralogous versions of seven ribosomal proteins (S14, S18, L28, L31, L32, L33, and L36), which differ in their potential to bind structural zinc. The paralogues are termed C + or − on the basis presence absence putative cysteine ligands. Here, mutational studies suggest that version L31 can functionally replace its paralogue only when expressed at an artificially elevated level. We show level expression four transcriptional units encoding is under...