K. A. Jolley

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.

Core genome MLST for epidemiological and evolutionary analyses of phytopathogenic Xanthomonas citri

This paper develops a core genome MLST scheme for Xanthomonas citri to improve epidemiological and evolutionary analysis of plant pathogens.

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

The paper identifies amino acid substitutions in penicillin binding proteins (PBPs) PBP1 and PBP3 as a mechanism of cephalosporin resistance in C. difficile, which co-occurs with fluoroquinolone resistance in epidemic lineages.

Genomic library of Bordetella

The paper creates a unified genomic library of Bordetella strains, revealing new species and phylogenetic insights, and provides resources for studying Bordetella evolution and epidemiology.

Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

The paper quantifies horizontal gene transfer (HGT) between Campylobacter species with different host ecologies, showing cohabitation in the same host increases HGT by 6-fold.

A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains

The paper introduces a dual barcoding system for bacterial strain classification using Klebsiella pneumoniae genomes, defining sublineages with genetic dissimilarity thresholds and providing a publicly accessible taxonomy platform.

Establishment of a publicly available core genome multilocus sequence typing scheme for Clostridium perfringens

This paper establishes a core genome MLST scheme for C. perfringens and applies it to poultry and non-poultry strains to identify clustering patterns and associations with netB gene carriage and clinical disease.

A two-hit epistasis model prevents core genome disharmony in recombining bacteria

The paper shows that recombination in bacteria can overcome genomic disharmony through a two-hit epistasis model, allowing beneficial gene combinations to be reinstated in new genetic backgrounds.

Domestication of Campylobacter jejuni NCTC 11168

This study compares genetic and phenotypic variation in 23 isolates of the reference Campylobacter jejuni strain NCTC 11168, showing significant genomic and phenotypic differences despite being considered identical.