Kelly L. Wyres

A capsule polysaccharide synthesis locus database for the Klebsiella oxytoca Species Complex

A curated Kaptive-compatible database of 88 capsule (K) loci types 97.6% of dereplicated Klebsiella oxytoca species complex genomes, versus 50.3% typed with the existing K. pneumoniae database.

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.

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports co-existence of diverse lineages

This study maps metabolic diversity in Klebsiella pneumoniae sub-lineages using genomics and metabolic modeling, revealing lineage-specific metabolic profiles that support coexistence through cross-feeding.

Anti-capsule human monoclonal antibodies protect against hypervirulent and pandrug-resistant Klebsiella pneumoniae

This study isolates human monoclonal antibodies against hypervirulent, pandrug-resistant Klebsiella pneumoniae and identifies capsule-specific antibodies as protective against bloodstream infection.

IS-capades of Klebsiella pneumoniae: Insertion sequences drive metabolic loss in obscure sub-lineages

The paper investigates the relationship between insertion sequences (IS) and metabolic capacity in four Klebsiella pneumoniae sub-lineages, finding higher IS loads correlate with reduced metabolic gene numbers and substrate utilisation.

Fast and Accurate in silico Antigen Typing with Kaptive 3

Kaptive v3 improves antigen typing accuracy and speed for KpSC genomes by addressing assembly fragmentation issues, enabling efficient in silico serotyping.

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.

Genomic and functional analysis of rmp locus variants in Klebsiella pneumoniae

The paper analyzes the genetic diversity and functionality of rmpADC variants in Klebsiella pneumoniae to understand their role in virulence and antimicrobial resistance.

A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex

This paper constructs a comprehensive pangenome-scale metabolic model for the Klebsiella pneumoniae species complex, showing improved accuracy in growth predictions compared to previous models.

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.

Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae

This study evaluates ONT-only assemblies for genomic surveillance of Klebsiella pneumoniae, showing reliable MLST, K type, and AMR detection but challenges in cluster detection.

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.

Kaptive 2.0: updated capsule and LPS locus typing for the Klebsiella pneumoniae species complex

Kaptive 2.0 updates capsule and LPS locus typing for Klebsiella pneumoniae by adding novel sequences and improving O2 antigen prediction, enabling better surveillance and control strategies.

Trycycler: consensus long-read assemblies for bacterial genomes

Trycycler improves bacterial genome assemblies by combining multiple long-read assemblies, reducing errors and improving accuracy when followed by polishing with Medaka and Pilon.

Recovery of small plasmid sequences via Oxford Nanopore sequencing

This study compares Oxford Nanopore ligation and rapid library preparation methods for bacterial genome sequencing, finding that rapid methods better recover small plasmids.

Genomic surveillance framework and global population structure for Klebsiella pneumoniae

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

Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in Klebsiella pneumoniae

The paper investigates t(m)DNAs as integration sites for genomic islands and prophages in Klebsiella pneumoniae, finding their role in horizontal gene transfer and genome evolution.

Convergence of virulence and multidrug resistance in a single plasmid vector in multidrug-resistant Klebsiella pneumoniae ST15

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.

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.

Yersiniabactin, Colibactin and Wider Resistome Contribute to Enhanced Virulence and Persistence of KPC-2-Producing Klebsiella pneumoniae CG258 in South America

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.

Population genomics of hypervirulent Klebsiella pneumoniae clonal group 23 reveals early emergence and rapid global dissemination

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.

Best Practice Data Life Cycle Approaches for the Life Sciences

The paper provides best practice data life cycle approaches for life sciences researchers focusing on omics datasets and computational data analysis.

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.