Background: Phage-encoded Shiga toxins, the hallmark feature of Shiga toxin-producing Escherichia coli (STEC), are linked to varying clinical severity. Subtype stx2a is associated with a higher risk of progression from foodborne gastroenteritis to severe haemolytic uraemic syndrome (HUS). Methods: 19,429 E. coli genomes submitted to UKHSA between 2016-2024 were extracted from EnteroBase, with serotype and stx information per isolate obtained from UKHSA and additional stx subtyping performed using StxTyper. Serotype distributions were quantified in R and visualised using Grapetree. Gene-level variation was identified using snp-sites, quantified with VCFtools and phylogenetic relationships inferred using IQ-Tree. Prophage regions were extracted using PHASTEST and annotated using Pharokka. Results: Overall, stx2a was present in 40.0% (n=4114) of STEC isolates across 76 O serogroups, most commonly in O157 (n = 2274, 17.7%), O26 (n = 824, 6.4%) and O145 (n= 562, 4.4%), with increasing prevalence over time in unique non-O157 serogroups. stx2a was most commonly observed alone, in 18.4% (n=2375) of isolates and within 16 additional stx subtype combinations. Gene level analysis identified 89 SNPs with multiple allelic variants clustering by serotype, with additional diversity in further stx presence alongside stx2a. Phage-level analyses integrated with gene level and genomic context data demonstrate connections between serotype and stx2a variants.