Julian Parkhill

This study traces the evolutionary path from ST131-B to ST131-C clades in E. coli by analyzing genomic data from ST131-B0 isolates, revealing genetic changes associated with antibiotic resistance and host adaptation.

This study identifies mutagens and host antiviral proteins as major contributors to hantavirus mutagenesis, influencing mutation patterns and genetic diversity.

This study tracks the 28-year evolution of a Burkholderia pseudomallei strain in sterile water, identifying genetic changes and metabolic adaptations to nutrient-depletion.

The paper analyzes defence system interactions in Pseudomonas aeruginosa genomes to understand their role in shaping accessory genome dynamics and ecological patterns.

This study uses mutational spectra to infer influenza virus transmission routes and adaptive mutations enabling sustained respiratory transmission.

This study analyzes 585 Streptococcus canis isolates to identify genetic factors driving its expansion, finding two dominant lineages associated with increased pathogenicity and host adaptation through genetic exchange with other streptococcal species.

This study characterizes Ornithobacterium hominis colonization dynamics in a South African birth cohort, revealing its microbiome interactions and genetic features.

This paper uses minimal machine learning models to predict antibiotic resistance in Klebsiella pneumoniae and identifies gaps in existing AMR databases for novel marker discovery.

The paper analyzes the mutational landscape of Staphylococcus aureus during colonization, identifying adaptive mutations in metabolic pathways and antibiotic targets.

The paper introduces MutTui, a tool to calculate and compare mutational spectra of DNA and RNA pathogens using multiple sequence data types.

The paper uses whole genome sequences and movement data to infer M. bovis transmission routes between cattle and badgers, finding higher cattle-to-cattle and badger-to-badger transmission rates than between species.

The paper analyzes B. pertussis genotype dynamics post-vaccine policy changes, showing fitness shifts and regional diversity patterns.

The paper identifies high within-lineage genomic diversity and gene content differences in Mycobacterium tuberculosis complex lineage 5 compared to H37Rv, affecting transmission analysis and suggesting the need for alternative reference genomes.

This study uses whole genome sequencing to analyze the population structure and transmission patterns of Mycobacterium bovis in Ethiopia, identifying two distinct introductions of the Eu3 clonal complex from Europe.

The paper analyzes genomes of Mycobacterium africanum strains to identify a new lineage and explore their evolutionary history and phylogeography.

Panaroo's graph-based pangenome clustering uses gene adjacency across genomes to correct annotation errors, shrinking spurious accessory genomes and enlarging core genomes in simulated and real bacteria.

The paper analyzes global E. coli ST131 genomes to trace the evolution and spread of antibiotic-resistant subclones, identifying a C2 lineage that displaced a C1 strain in an Irish LTCF.

The paper evaluates GWAS methods for detecting antibiotic resistance in Staphylococcus aureus genomes, finding they identify novel resistance mutations but are less accurate than literature-based approaches.

This study traces the evolutionary divergence of Neisseria gonorrhoeae by analyzing global isolates, linking antimicrobial use to the emergence of two distinct lineages with different resistance strategies.

This paper introduces SpydrPick, a model-free method to detect co-selection and epistasis in bacterial genomes, revealing both known and novel targets in human pathogens.

The paper introduces mSWEEP, a method for high-resolution bacterial lineage quantification from plate sweeps, showing improved accuracy in detecting and estimating abundances of bacterial lineages.

The paper uses genome-wide association studies to show human and pneumococcal genetic variation influences susceptibility and severity of pneumococcal meningitis.

This study uses long-read sequencing to assemble E. coli ST131 genomes, revealing diverse plasmid and chromosomal contexts of antibiotic resistance genes.

The paper reports the discovery of a new bacterial species, Candidatus Ornithobacterium hominis, identified from nasopharyngeal swabs and describes its genomic features and colonization patterns.

The paper compares E. coli isolates from humans and livestock to assess transmission and resistance gene sharing, finding genetic distinctions and limited shared antimicrobial resistance genes.

This study identifies negative frequency-dependent selection in Escherichia coli ST131 as a key driver of its evolutionary success and adaptation to different ecological niches.

The paper uses TraDIS to identify genes involved in twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa, revealing both known and novel components.

The paper uses whole genome sequencing to analyze invasive GBS isolates in the Netherlands and identifies the expansion of a CC17 sub-lineage, CC17-1A, as correlated with increased disease incidence.

The paper compares the genomes of Mycobacterium africanum Lineage 5 and 6 from Ghana, finding genomic diversity and selection pressure differences suggesting distinct ecological niches.