Timothy J. Dallman

The paper benchmarks pangenome graph construction methods using Escherichia coli O157:H7 genomes, showing that representation strategies and assembly completeness significantly affect graph topology and accuracy.

This paper analyzes STEC population structure and host-disease associations using whole genome sequencing of 3,418 isolates from 11 European countries, identifying distinct subpopulations linked to disease severity.

The paper identifies a prophage-encoded sRNA, HnrS, that counteracts xenogenic silencing by repressing Hha, enabling virulence gene expression in E. coli.

This study traces the global spread of Listeria monocytogenes clonal complex 1 (Lm-CC1) through historical data, identifying two waves of expansion linked to livestock trade and cattle farming.

This study constructs a phylogenetic tree of 131 S. Typhimurium strains to reveal population structure and adaptation to domesticated and wild animal hosts.

The paper compares stx2a-encoding prophages in UK STEC O157:H7 sub-lineages, finding high diversity and independent acquisition, while stx2c-encoding prophages show vertical inheritance.

The paper identifies a multi-drug resistant Shigella sonnei strain as the cause of persistent shigellosis in England, linked to sexual transmission among men who have sex with men.

SnapperDB provides tools for storing and analyzing bacterial variant data to enable scalable and reproducible SNP analysis of microbial populations.