Adam W. J. Jenney

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

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.

Wild type domestication: loss of intrinsic metabolic traits concealed by culture in rich media

The paper identifies hidden metabolic mutations in Klebsiella pneumoniae cultures grown in rich media, showing how these mutations can persist undetected and affect auxotrophy.

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.

Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models

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

ESBL plasmids in Klebsiella pneumoniae: diversity, transmission, and contribution to infection burden in the hospital setting

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.

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

This study identifies and tracks virulence loci encoding siderophore synthesis in K. pneumoniae using genomic surveillance tools.

Identification of Klebsiella capsule synthesis loci from whole genome data

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.