Nicholas Robert Thomson

Phylo-Plex is a low-cost amplicon sequencing method for high-resolution genomic epidemiology, achieving fine-scale lineage discrimination comparable to whole-genome sequencing in resource-limited settings.

This study develops a human epithelial co-culture system that supports Treponema pallidum growth and identifies two distinct host-cell interaction behaviors.

The paper identifies non-coli Escherichia species, including clade I ST485, that carry EAEC virulence genes and are often misidentified as E. coli, highlighting their potential role in diarrheal disease.

This study refines SPATE gene detection in EAEC genomes, revealing phylogeny-associated differences in SPATE distribution and identifying pic as a diarrhoea-associated gene.

This study tracks the 28-year evolution of a Burkholderia pseudomallei strain in sterile water, identifying genetic changes and metabolic adaptations to nutrient-depletion.

This study uses RNA-sequencing to generate a high-quality transcriptome profile of Treponema pallidum subsp. pallidum, confirming transcription of previously hypothetical genes and revealing new gene organization features.

This study analyzes 1,853 Aeromonas genomes, revealing high genetic diversity, widespread AMR genes, and frequent misidentification as Vibrio cholerae.

This study characterizes the genetic diversity and virulence factors of EPEC in southwestern Nigeria using whole-genome sequencing, identifying prevalent serotypes and potential outbreaks.

This paper introduces WRAPs, designed proteins that solubilize membrane proteins without detergents, enabling structural studies and vaccine development.

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

The paper uses whole genome sequencing to show high diversity and transmission of ESBL-Ec across human, animal, and environmental compartments in low-income settings, supporting the One Health approach for AMR control.

The paper compares plasmids from pre-antibiotic era bacteria with modern plasmids to show how resistance genes evolved and spread over time.

The paper introduces genetically encoded fluorescent tags for Treponema pallidum and Sf1Ep cells to enhance visualization and study host-pathogen interactions in syphilis research.

This study investigates the genomic structure and evolution of Salmonella ST34 in Southeast Asia, showing that multidrug resistance plasmids drive its clonal expansion and international spread.

Panakeia provides a detailed and user-friendly analysis of bacterial pangenomes, offering insights into structural patterns and biological diversity.

The paper performs a genomic analysis of Vibrio cholerae El Tor strains from Bangladesh, identifying two lineages, BD-1 and BD-2, and their distinct genomic traits and epidemiological implications.

This study compares serotyping and cgMLST for Shigella classification, finding that cgMLST better reflects genetic relationships.

The paper uses PFGE to analyze V. cholerae El Tor strains from Bangladesh and other countries, finding most pandemic strains belong to a major clade with distinct geographic lineages.

The paper presents a population structure-aware method to classify genes in a bacterial pan-genome, revealing distinct evolutionary dynamics in 7,500 E. coli genomes.

This paper curates a high-quality collection of over 10,000 E. coli and Shigella genomes to facilitate analysis of genetic diversity and lineage differences.

The paper shows that macrolide resistance in syphilis emerged independently in multiple lineages, not just the SS14 lineage, challenging the idea that resistance drove its spread.

This study reports whole-genome sequencing and antimicrobial resistance analysis of Klebsiella pneumoniae isolates from the Caribbean, revealing carbapenem resistance and hypervirulent strains.

rPinecone defines sub-lineages in low-variant bacterial populations using phylogenetic trees to improve outbreak and endemic disease analysis.

PlasmidTron identifies mobile genetic elements linked to phenotypes by analyzing short read WGS data and phenotypic metadata from bacterial populations.

The paper analyzes Ct genomic diversity and identifies SNPs associated with ocular localization and disease severity in a West African trachoma-endemic population.

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.