Ben Pascoe

Publications

• Assessing the pathogenic potential of less common Salmonella enterica serotypes circulating in the Thai pork production chain
• Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease
• Molecular evidence for cross boundary spread of Salmonella spp. in meat sold at retail markets in the middle Mekong basin area
• A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk
• The emergence of plasmid-borne cfr-mediated linezolid resistant-staphylococci in Vietnam
• Stress-resistance associated with multi-host transmission and enhanced biofilm formation at 42 °C among hyper-aerotolerant generalist Campylobacter jejuni
• Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA
• Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry
• Prevalence of faecal carriage of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in veterinary hospital staff and students
• Genomic epidemiology of clinical Campylobacter spp. at a single health trust site
• Genome-wide identification of host-segregating SNPs for source attribution of clinical Campylobacter coli isolates
• Stereoselective Bacterial Metabolism of Antibiotics in Environmental Bacteria – A Novel Biochemical Workflow
• Local accessory gene sharing drives lineage-specific acquisition of antimicrobial resistance in Egyptian Campylobacter spp.
• Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages
• Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis
• Whole-genome characterisation of multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand
• Multiple hypervirulent methicillin-sensitiveStaphylococcus aureuslineages contribute towards poor patient outcomes in orthopedic device-related infections
• A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas
• Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon
• Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages
• Occurrence and sequence type of antimicrobial resistant Salmonella spp. circulating in antibiotic-free organic pig farms of northern-Thailand
• Multiple clones of colistin-resistant Salmonella enterica carrying mcr-1 plasmids in meat products and patients in Northern Thailand
• Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter
• Non-serotype 2 isolates from healthy pigs are a potential zoonotic reservoir of Streptococcus suis genetic diversity and antimicrobial resistance
• Domestication of Campylobacter jejuni NCTC 11168
• Hermes: an ensemble machine learning architecture for protein secondary structure prediction
• Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain
• Identification of Streptococcus suis carriage in healthy pigs in Chiang Mai, Thailand
• Stereoselective metabolism of chloramphenicol by bacteria isolated from wastewater, and the importance of stereochemistry in environmental risk assessments for antibiotics
• Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon
• Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni
• High-resolution sweep metagenomics using fast probabilistic inference [version 2; peer review: 2 approved]
• Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance
• Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades
• Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations
• Occurrence and sequence type of antimicrobial resistant Salmonella spp. circulating in antibiotic-free organic pig farms of northern-Thailand
• Genome-based analysis of infrequent Salmonella serotypes through the Thai pork production chain
• Characterisation of Salmonella enterica clones carrying mcr-1 plasmids in meat products and patients in Northern Thailand using long read sequencing
• Genome evolution and the emergence of pathogenicity in avian Escherichia coli
• Spatiotemporal Investigation of Antibiotic Resistance in the Urban Water Cycle Influenced by Environmental and Anthropogenic Activity
• Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates
• Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans
• A two-hit epistasis model prevents core genome disharmony in recombining bacteria
• Oral and gut microbiome biomarkers of susceptibility to respiratory tract infection in adults: a longitudinal cohort feasibility study
• Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter
• Domestication of Campylobacter jejuni NCTC 11168
• Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease
• Genetic Diversity of Composite Enterotoxigenic Staphylococcus epidermidis Pathogenicity Islands
• High-resolution sweep metagenomics using fast probabilistic inference
• Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli
• High-resolution sweep metagenomics using fast probabilistic inference
• Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork
• Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations
• From Escherich to the Escherichia coli genome
• Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil
• Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group
• Convergent Amino Acid Signatures in Polyphyletic Campylobacter jejuni Subpopulations Suggest Human Niche Tropism
• Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork
• Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations
• Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins
• The Potential of Isolation Source to Predict Colonization in Avian Hosts
• Genome-wide identification of host-segregating epidemiological markers for source attribution in Campylobacter jejuni
• Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B) Genes
• Bayesian identification of bacterial strains from sequencing data
• Recombination-mediated host-adaptation by avian Staphylococcus aureus
• A comparative genomics study of Staphylococcus epidermidis from orthopedic device-related infections correlated with patient outcome
• Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork
• Local genes for local bacteria
• Correction
• High resolution whole genome multilocus sequence typing (wgMLST) schemes for Salmonella enterica Weltevreden epidemiologic investigations
• Hidden antibiotic resistance fitness costs revealed by GWAS-based epistasis analysis
• Genetic and chemical differentiation of Campylobacter coli and Campylobacter jejuni lipooligosaccharide pathways
• Genetic features of livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs that carry the lsa(E) gene for quinupristin/dalfopristin resistance
• Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections
• DNA extraction: Campylobacter
• Dormant Cells of Staphylococcus aureus Are Resuscitated by Spent Culture Supernatant.
• The zinc-responsive regulator Zur controls expression of the coelibactin gene cluster in Streptomyces coelicolor
• Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples.
• Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations
• Can crab shells protect roses from blackspot?
• Genomes of Helicobacter pylori prophages
• Can crab shells protect roses from blackspot?
• A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic campylobacter.
• Staphylococcus epidermidis in Biomaterial-Associated Infections
• Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species.
• Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.
• Persistent Staphylococcus aureus Isolates from Two Independent Cases of Bacteremia Display Increased Bacterial Fitness and Novel Immune Evasion Phenotypes.
• Progressive genome-wide introgression in agricultural Campylobacter coli
• Mechanisms of Staphylococcus epidermidis biofilm formation in different types of biomaterial-related infections
• Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and σR
• Draft Genome Sequence of an Enterobacter Species Associated with Illnesses and Powdered Infant Formula.
• Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni
• Large sequence diversity within biosynthesis locus and common biochemical features of Campylobacter coli lipooligosaccharides.
• Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
• Does Biofilm Formation Aid Colonization and Infection in Campylobacter?
• Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs.
• Genome-based analysis of infrequent Salmonella serotypes through the Thai pork production chain.
• Colistin resistance and resistance determinants are mobile among Salmonella enterica isolates from diseased and healthy pigs in Thailand
• Contrasting genes conferring short and long-term biofilm adaptation in Listeria
• Investigation of swine caecal microbiomes in the northern region of Thailand
• Urbanization spreads antimicrobial resistant enteric pathogens in wild bird microbiomes
• Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study
• Lineage‐specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group
• Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations.
• Contrasting genes conferring short- and long-term biofilm adaptation in Listeria.
• Author Correction: Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations.
• C-SOP-201: Genomic DNA Quantification using a Qubit Fluorometer v1
• Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork
• Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes
• Genomic resistant determinants of multidrug resistant Campylobacter spp. isolates in Peru
• Recombination-mediated dissemination of Methicillin-resistant S. aureus clonal complex 1 in the Egyptian health care settings
• The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
• Epistasis, core-genome disharmony, and adaptation in recombining bacteria
• C-SOP-1001: High Molecular Weight DNA (HMW DNA) Extraction from Bacteria using NEB Monarch HMW DNA extraction kit v1
• Quantifying bacterial evolution in the wild: a birthday problem forCampylobacterlineages
• Multiple clones of colistin-resistantSalmonella entericacarryingmcr-1plasmids in meat products and patients in Northern Thailand
• Antimicrobial resistantSalmonellaspp. circulating in antibiotic-free organic pig farms of northern-Thailand
• Global Variation in Escherichia coli mcr-1 Genes and Plasmids from Animal and Human Genomes Following Colistin Usage Restrictions in Livestock
• Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool.
• Geographical distribution, disease association and diversity of Klebsiella pneumoniae K/L and O antigens in India: roadmap for vaccine development
• Contrasting genes conferring short-and long-term biofilm adaptation in Listeria
• Author Correction: Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations (Nature Communications, (2022), 13, 1, (6842), 10.1038/s41467-022-34475-3)
• High-resolution sweep metagenomics using fast probabilistic inference [version 1; peer review: 1 approved, 1 approved with reservations]
• Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs
• Multiple hypervirulent methicillin-sensitive Staphylococcus aureus lineages contribute towards poor patient outcomes in orthopedic device-related infections
• Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli (Nature Communications, (2021), 12, 1, (765), 10.1038/s41467-021-20988-w)
• Machine Learning the Source Campylobacter Infection in the United States of America
• Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations
• Molecular evidence for cross boundary spread of Salmonella spp. In meat sold at retail markets in the middle Mekong basin area
• Genomic resistant determinants of multidrug-resistant Campylobacter spp. isolates in Peru
• Salmonella linkaged between good agricultural practice certified broiler farms and poultry slaughterhouses in an intensive farming area in upper northern part of Thailand
• Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves zur and σR
• Comparative genomics study of Staphylococcus epidermidis isolates from orthopedic-device-related infections correlated with patient outcome
• Recombination-mediated host adaptation by avian staphylococcus aureus
• Draft genome sequence of an Enterobacter species associated with illnesses and powdered infant formula
• Large sequence diversity within the biosynthesis locus and common biochemical features of Campylobacter coli lipooligosaccharides
• Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis
• Hidden antibiotic resistance fitness costs revealed by GWAS-based epistasis analysis.
• Biofilm morphotypes and population Structure among Staphylococcus epidermidis from commensal and clinical samples
• Erratum: Biofilm morphotypes and population structure among staphylococcus epidermidis from commensal and clinical samples (PLoS ONE (2016) 11:3 (e0151240) DOI: 10.1371/journal.pone.0151240)
• Hermes: An ensemble machine learning architecture for protein secondary structure prediction
• Whole-genome characterisation of multidrug resistant monophasic variants of salmonella typhimurium from pig production in Thailand
• Genome-Wide Identification of Host-Segregating Single-Nucleotide Polymorphisms for Source Attribution of Clinical Campylobacter coli Isolates
• Genome comparison of erythromycin resistant campylobacter from Turkeys identifies hosts and pathways for horizontal spread of erm(B) genes
• Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations
• Domestication of campylobacter jejuni NCTC 11168
• Psychometric evaluation of the near activity visual questionnaire presbyopia (NAVQ-P) and additional patient-reported outcome items
• Machine learning to attribute the source of Campylobacter infections in the United States: a retrospective analysis of national surveillance data
• Assessing antimicrobial resistance profiles of Salmonella enterica in the pork production system
• The epidemiology and impact of persistent Campylobacter infections on childhood growth among children 0–24 months of age in resource-limited settings