J. Parkhill

Integrating bacterial genomics and host transcriptomics links Burkholderia pseudomallei variation to melioidosis mortality and neutrophil responses

The spatiotemporal distribution of human pathogens in ancient Eurasia and the emergence of zoonotic diseases

The paper maps ancient pathogens in Eurasia, showing zoonotic diseases emerged with livestock domestication and spread with pastoralist migrations.

Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in northeast Thailand

This study identifies three dominant B. pseudomallei lineages in northeast Thailand, their environmental persistence, and factors driving their geographic spread.

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

The paper uses transposon mutagenesis across Enterobacteriaceae species to identify core essential genes and shows rapid turnover of essentiality across related strains.

Mutational spectra distinguish SARS-CoV-2 replication niches

The paper analyzes SARS-CoV-2 mutational spectra to infer replication niches, finding reduced G>T mutations in Omicron linked to upper respiratory tract replication.

Mutational spectra analysis reveals bacterial niche and transmission routes

The paper analyzes mutational spectra in bacterial lineages to infer niche-specific mutagen exposure and transmission routes.

A scalable analytical approach from bacterial genomes to epidemiology

The paper presents a scalable approach for genomic epidemiology analyses of bacterial pathogens, emphasizing the construction of dated phylogenies and computational efficiency.

The pathobiology of Mycobacterium abscessus revealed through phenogenomic analysis

This study uses phenogenomic analysis to uncover virulence mechanisms and drug resistance in Mycobacterium abscessus by integrating phenotyping, genomics, and computational modeling.

A two-hit epistasis model prevents core genome disharmony in recombining bacteria

The paper shows that recombination in bacteria can overcome genomic disharmony through a two-hit epistasis model, allowing beneficial gene combinations to be reinstated in new genetic backgrounds.

Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella

This study identifies virulence determinants of multidrug-resistant Klebsiella pneumoniae using Galleria mellonella infection model, highlighting surface polysaccharides and NfeR as key factors.

Screening for highly transduced genes in Staphylococcus aureus reveals both lateral and specialized transduction

The paper screens a transposon mutant library in Staphylococcus aureus to identify genes enhancing transduction by phage φ11, revealing both lateral and specialized transduction mechanisms.

Co-evolutionary signals from Burkholderia pseudomallei genomics identify its survival strategies and highlight improving environmental health as prevention policy

This study identifies co-selected gene pairs in Burkholderia pseudomallei genomes that enhance survival under nutrient stress, linking environmental factors to melioidosis prevalence.

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

The paper identifies and characterizes small proteins in Salmonella Typhimurium using integrated omics data, revealing a new role for MgrB in virulence and motility.

A comprehensive portrait of antimicrobial resistance in the zoonotic pathogen Streptococcus suis

This study examines antimicrobial resistance in Streptococcus suis using MIC measurements and whole-genome sequencing, identifying resistance determinants and highlighting the complexity of resistance mechanisms.

Kill and cure: genomic phylogeny and bioactivity of a diverse collection of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles

This study examines the genomic phylogeny and bioactivity of 206 Burkholderia gladioli strains, identifying toxin-producing clades and potential therapeutic strategies for CF-related infections.

Genomic analysis of carbapenemase-encoding plasmids from Klebsiella pneumoniae across Europe highlights three major patterns of dissemination

This study analyzes carbapenemase-encoding plasmids in K. pneumoniae across Europe using long-read sequencing, identifying three distinct dissemination patterns of resistance genes.

Discovery of a Pseudomonas aeruginosa Type VI secretion system toxin targeting bacterial protein synthesis using a global genomics approach

The paper uses TraDIS to identify T6SS toxins in Pseudomonas aeruginosa, finding Tse8 targets bacterial protein synthesis by disrupting the transamidosome complex.

Engineering bacteriocin-mediated resistance against plant pathogenic bacteria in plants

This paper demonstrates that expressing the bacteriocin putidacin L1 in plants provides effective resistance against Pseudomonas syringae and related pathogens.

Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae

This study examines genetic variation in Restriction-Modification systems across 25 Neisseria gonorrhoeae strains, revealing differences in RMS activity and methylation targets.

Domestication of Campylobacter jejuni NCTC 11168

This study compares genetic and phenotypic variation in 23 isolates of the reference Campylobacter jejuni strain NCTC 11168, showing significant genomic and phenotypic differences despite being considered identical.

The speciation and hybridization history of the genus Salmonella

This study investigates the speciation and hybridization history of Salmonella, identifying eleven phylogroups and revealing complex hybridization events that challenge traditional speciation models.

Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana

This study analyzes Mycobacterium bovis isolates from Ghana using whole-genome sequencing to identify risk factors and genetic characteristics associated with bovine tuberculosis.

Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli

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 capsule regulatory network of Klebsiella pneumoniae defined by density-TraDISort

This study identifies genes regulating capsule production in K. pneumoniae using density-TraDISort, revealing a complex regulatory network involving multiple global regulators.

Methicillin resistant Staphylococcus aureus emerged long before the introduction of methicillin in to clinical practice

This study shows that MRSA emerged in the mid-1940s, long before methicillin was introduced, due to prior use of first-generation beta-lactams.