Harry A. Thorpe

High frequency body site translocation of nosocomial Pseudomonas aeruginosa

This study investigates the translocation of Pseudomonas aeruginosa between body sites in hospitalized patients, finding that clones often move from the respiratory tract to the gut.

Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli

The paper investigates the evolutionary dynamics of colibactin production and resistance in E. coli, showing clonal expansions linked to co-evolution between production and immunity.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

Enhanced metagenomics-enabled transmission inference with TRACS

TRACS improves transmission inference by accurately estimating SNP-level genetic distances, outperforming existing methods in multiple datasets and revealing species-specific transmission rates between mothers and infants.

PAN-GWES: Pangenome-spanning epistasis and co-selection analysis via de Bruijn graphs

PAN-GWES identifies co-selected and epistatic genomic variations in bacterial genomes using de Bruijn graphs to analyze drug resistance and adaptation traits.

Detecting co-selection through excess linkage disequilibrium in bacterial genomes

The paper introduces LDWeaver, a method to detect co-selection in bacterial genomes by analyzing both short- and long-range linkage disequilibrium, and validates findings using functional annotation and phenotypic measurements.

Convergence and global epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus.

The paper characterizes iuc3-carrying plasmids in Klebsiella pneumoniae isolates, identifying convergent plasmids with resistance and virulence genes and highlighting their global epidemiology.

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

The paper estimates molecular clock rates in Campylobacter using a birthday problem analogy to quantify lineage turnover and diversification in environmental bacteria.

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

PIRATE clusters and classifies orthologous gene families in bacterial pangenomes across sequence similarity thresholds and scales efficiently with large datasets.

Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria

Piggy analyzes intergenic regions in bacterial pan-genomes, showing divergent IGRs correlate with gene expression differences in Staphylococcus aureus.