K. A. Jolley

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

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.

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.

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.

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.

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.

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.

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.