K. L. Wyres

Life Identification Numbers: A bacterial strain nomenclature approach

The paper proposes the Life Identification Number (LIN) system as a stable, multilevel strain taxonomy for bacterial pathogens based on core genome MLST to improve epidemiological tracking and nomenclature consistency.

Transmission of Klebsiella strains and plasmids within and between Grey-headed flying fox colonies

This study identifies transmission clusters and plasmid exchange among Klebsiella strains in Grey-headed flying foxes, showing gene flow between bat and human-associated isolates.

Linear plasmids in Klebsiella and other Enterobacteriaceae

This study identifies and characterizes linear plasmids in Klebsiella pneumoniae and other Enterobacteriaceae, revealing their phylogenetic diversity and potential for horizontal transfer.

A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality

The paper curates 37 strain-specific genome-scale metabolic models for Klebsiella pneumoniae species complex isolates, revealing strain-specific metabolic differences and gene essentiality.

A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-2015: Introduction and spread of ESBL facilitated by CG15 and CG307

This study analyzes the genomic changes in Klebsiella pneumoniae in Norway from 2001-2015, identifying the spread of ESBL-producing strains driven by CG307 and CG15.

Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian Fruit Bats (Pteropus poliocephalus)

This study identifies novel Klebsiella africana and Klebsiella pneumoniae strains in Australian fruit bats, finding low antimicrobial resistance and no hypervirulent or MDR strains.

Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

The paper identifies hidden transmission of a carbapenemase-producing Klebsiella pneumoniae strain using genomic and metagenomic data from multiple studies.

Detection of plasmid contigs in draft genome assemblies using customized Kraken databases

This paper introduces a method using Kraken with a custom database to detect plasmid contigs in bacterial genome assemblies, showing improved performance over existing tools.

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

The paper investigates the diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales using comparative genomics across 27,334 genomes, revealing dynamics driven by horizontal gene transfer and selective preservation.

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive

This paper creates curated databases for Acinetobacter baumannii capsular polysaccharide and outer core loci, compatible with Kaptive, and validates their utility in typing genome assemblies.

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia.

This study identifies diverse antimicrobial resistant and hypervirulent Klebsiella pneumoniae strains in South and Southeast Asia, highlighting the convergence of AMR and virulence genes.

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae

The paper compares the evolutionary dynamics of horizontal gene transfer in drug-resistant and virulent Klebsiella pneumoniae clones to assess the risk of gene convergence.

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

The paper tracks the emergence and global spread of a CTX-M-15-producing K. pneumoniae strain ST307, showing it originated in the mid-1990s and is associated with a plasmid containing antimicrobial resistance genes.

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

The paper analyzes the prevalence and evolution of yersiniabactin-encoding mobile elements in Klebsiella pneumoniae using whole genome sequences, identifying diverse lineages and novel dispersal mechanisms.

Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes

Kaptive Web is an online tool for typing Klebsiella K and O loci in genome assemblies, showing extensive diversity in these loci among clinical isolates.

Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital

The paper investigates K. pneumoniae carriage and infection in geriatric wards, finding that most isolates originated from patients' gut microbiomes, while ESBL strains were acquired in the referring hospital.