Keith A. Jolley

Emergence of short-lived meningococci causing focal epidemics can be associated with gene transfer from carriage-associated Neisseria

A 21-case nightclub-linked meningococcal outbreak variant differed from its closest relatives by horizontal gene transfer from carriage-associated Neisseria, affecting iron acquisition and type IV pili genes.

FlavoTyper: a genome-based in-silico serotyping tool for the fish pathogen Flavobacterium psychrophilum

FlavoTyper is a genome-based in-silico tool for serotyping Flavobacterium psychrophilum, showing strong association between O-types and host fish species.

High resolution Streptococcus pyogenes core genome MLST and LIN coding scheme for outbreak detection

The paper introduces a high-resolution core genome MLST and LIN coding scheme for Streptococcus pyogenes to improve outbreak detection through scalable and sharable genetic relatedness analysis.

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.

GeneScanner: profiling genetic variation across bacterial populations

GeneScanner links laboratory genetic mutations to natural population variation in bacteria, enabling genotype-phenotype association studies across large genome collections.

Genetic context drives evolution of divergent antibiotic survival phenotypes in Staphylococcus epidermidis

This study shows that antibiotic resistance and tolerance in Staphylococcus epidermidis are genetically linked but phenotypically distinct, shaped by complex epistatic interactions.

A Life Identification Number Barcoding (LIN Code) System for Neisseria meningitidis: high resolution multi-level typing of meningococci.

This paper introduces a WGS-based LIN code system for Neisseria meningitidis to enable high-resolution multi-level typing and improve molecular epidemiology.

A stable, hierarchical LIN code system for Campylobacter jejuni and Campylobacter coli: A unified genomic nomenclature for lineage-level typing and global surveillance.

Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system

The paper develops a cgMLST scheme and LIN code system to classify Moraxella catarrhalis lineages, revealing two divergent seroresistant and serosensitive lineages with distinct genetic and virulence characteristics.

Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus

The paper develops a cgMLST scheme and LIN code system for S. aureus to enable high-resolution genotyping and classification of genetic lineages.

Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature

The paper develops a multi-resolution lineage nomenclature for Neisseria gonorrhoeae using LIN codes to improve lineage identification and reflect population structure and antibiotic resistance associations.

Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure

The paper develops a genomic resource and clustering methods for pneumococcal population analysis using a large curated dataset of genomes.

Development and Implementation of a Core Genome Multilocus Sequence Typing (cgMLST) scheme for Haemophilus influenzae

This paper develops and validates a core genome MLST (cgMLST) scheme for Haemophilus influenzae using pangenome analysis and validates it with genomic datasets, showing high congruence with phylogenetic analysis.

Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial

The paper uses whole genome sequences and movement data to infer M. bovis transmission routes between cattle and badgers, finding higher cattle-to-cattle and badger-to-badger transmission rates than between species.

Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index: a Rapid and Accessible Tool that Exploits Genomic Data in Public Health and Clinical Microbiology Applications

Evolution of ST-4821 clonal complex hyperinvasive and quinolone-resistant meningococci: the next meningococcal pandemic?

The paper tracks the global spread of quinolone-resistant Neisseria meningitidis clone ChinaCC4821-R1-C/B, showing its expansion from China to other countries and potential for a global pandemic.

Heterogeneity Among Estimates Of The Core Genome And Pan-Genome In Different Pneumococcal Populations

The paper analyzes genome sequences of pneumococci from different populations to assess core and pan-genome variability, finding significant differences between Maela isolates and others.