Jane Hawkey

AMRgen is an R package that links antimicrobial resistance genotypes to phenotypes through data harmonization, analysis, and visualization, using surveillance data from priority pathogens.

The paper identifies pre-existing anti-prophage antibodies and bacterial heteroresistance as factors contributing to phage therapy failure in a patient with chronic infection.

Flex-It is a genotyping framework for S. flexneri that rapidly characterizes genotypes and resistance determinants from sequencing data, enabling standardized surveillance of its population structure and antimicrobial resistance.

This study characterizes the diversity and niche associations of plasmids in Klebsiella pneumoniae species complex isolates from human, animal, and marine sources, revealing distinct patterns of antimicrobial resistance and virulence gene distribution.

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

The paper investigates the relationship between insertion sequences (IS) and metabolic capacity in four Klebsiella pneumoniae sub-lineages, finding higher IS loads correlate with reduced metabolic gene numbers and substrate utilisation.

The study tracks genomic changes in wMel Wolbachia over six years in three Aedes aegypti populations and finds minimal evolution, supporting its stability as a biocontrol agent.

The paper provides 15 genomically characterized Shigella sonnei isolates representing diverse sub-clades, with complete genome sequences and public availability for research.

This paper demonstrates that CRISPR-Cas9 enrichment combined with Oxford Nanopore sequencing improves detection of AMR genes and MLST in patient samples compared to unenriched sequencing.

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

This paper constructs a comprehensive pangenome-scale metabolic model for the Klebsiella pneumoniae species complex, showing improved accuracy in growth predictions compared to previous models.

Bactabolize generates strain-specific bacterial metabolic models and growth predictions, outperforming existing tools for Klebsiella pneumoniae.

The paper identifies a plasmid (Plasmid A) that transmitted four times into different Klebsiella lineages, causing 50% of ESBL episodes and persisting for 3-6 years, contributing to 21% of ESBL+ infections.

Trycycler improves bacterial genome assemblies by combining multiple long-read assemblies, reducing errors and improving accuracy when followed by polishing with Medaka and Pilon.

This paper introduces a pan-genome graph structure and software tool, pandora, to analyze bacterial genomic variation across multiple isolates with higher SNP recovery and lower error rates than existing methods.

The paper compares fully Bayesian and hybrid methods for inferring demographic parameters in bacterial genomic data, finding hybrid methods are computationally efficient and reliable when data have strong temporal structure.

This study tracks the evolution of carbapenem resistance in Acinetobacter baumannii during a 45-day infection in a burn patient, identifying novel mutations in resistance genes and showing collateral resistance from exposure to other antibiotics.