Edward J. Feil

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 examines synonymous SNPs in E. coli to show strand and expression-dependent mutagenesis, finding that certain transitions are more frequent on the leading strand and influenced by gene expression.

This study identifies prophage-encoded receptor-binding proteins (RBPs) mediating capsule specificity in Klebsiella pneumoniae, revealing structural diversity and functional activity beyond classical depolymerases.

amr.watch provides an interactive platform to analyze and visualize AMR trends from global WGS data, enabling ongoing situational awareness for research and policy.

This study assesses the antimicrobial effects and AMR selection potential of non-antibiotic drugs on bacterial communities using metagenomic and metatranscriptomic analyses.

This study shows that non-antibiotic drugs enhance the selection of antimicrobial resistance when combined with ciprofloxacin, altering community composition and increasing resistance gene prevalence.

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

This paper optimizes machine learning prediction of MICs in Klebsiella pneumoniae by evaluating regression vs classification approaches based on antibiotic concentration levels.

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

The paper examines polymorphism in intergenic regions and four-fold degenerate sites in bacterial genomes to explain nucleotide compositional strand asymmetry, finding that FFS polymorphisms, not IRs, explain the asymmetry.

The paper introduces Pathogenwatch, a web tool for genomic surveillance of Klebsiella, showing it identifies drug-resistant clones and vaccine candidate O-types in genomes from low- and middle-income countries.

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

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

The paper introduces mSWEEP, a method for high-resolution bacterial lineage quantification from plate sweeps, showing improved accuracy in detecting and estimating abundances of bacterial lineages.

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