Claire L. Gorrie

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

The paper benchmarks 44 tools for plasmidome reconstruction from short-read assemblies in Klebsiella pneumoniae, finding PlaScope and MOB-suite as top performers.

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

The paper systematically evaluates key parameters affecting SNP-based transmission inference of MDROs, finding that using a closely-related reference genome and sliding-window analysis improves accuracy.

The paper uses genomic analysis to assess MDRO transmission within and across hospitals, finding high transmission rates for vanA VRE and linking genomic data with epidemiologic data to evaluate infection control.

This paper demonstrates using multiplexed MinION sequencing and hybrid assembly to complete bacterial genome assemblies, achieving fully resolved genomes with minimal manual intervention.

Unicycler scaffolds SPAdes short-read assembly graphs using long reads, producing more complete bacterial assemblies with fewer misassemblies than competing hybrid tools, even at low long-read depth.

The paper identifies 134 distinct Klebsiella capsule synthesis loci from whole-genome data, introduces a novel software tool for locus identification, and proposes a standardized nomenclature.