Ryan R. Wick

The paper introduces Kleborate, a tool for analyzing K. pneumoniae genomes, demonstrating its use in genomic surveillance and metagenomic analysis of gut samples.

GeneMates identifies horizontal gene co-transfer in bacteria using WGS data and controls for population structure to avoid spurious associations.

This study compares hybrid assemblies of bacterial genomes using Illumina and long-read sequencing technologies, finding that combining ONT and Illumina reads provides high-quality, low-cost genome reconstruction.

The paper shows improved metagenomic reference databases increase read classification rates and affect downstream microbiome analysis.

This study evaluates basecalling tools for Oxford Nanopore sequencing, finding that taxon-specific training and larger neural networks improve accuracy, though polishing with Nanopolish reduces tool differences.

The paper identifies two Klebsiella pneumoniae isolates with convergent virulence and multidrug resistance genes on a single plasmid, highlighting the risk of rapid emergence of hypervirulent multidrug-resistant strains.

Deepbinner improves Oxford Nanopore demultiplexing by using deep learning on raw electrical signals, achieving high precision and low unclassified read rates.

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

This study identifies yersiniabactin, colibactin, and an expanded resistome as factors contributing to the enhanced virulence and persistence of KPC-2-producing K. pneumoniae CG258 in South America.

This study analyzes the population genomics of hypervirulent Klebsiella pneumoniae clonal group 23, revealing its early emergence and global spread through genomic analysis of 98 isolates.

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.

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.